Travel to Japan for first time

Don't drive. Everyone takes the trains, or subways within a city.
Kyoto must not be missed, it's the spiritual (and historical) capital of Japan, with many of the structures/gardens/etc that survived the fire-bombings of WW2.
Tokyo has few historical sites that pre-date the 1940's because it was extensively fire-bombed in 1944-45.

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Japan is a wonderful country to visit.

1. Many Japanese speak English. The Japanese people are very nice, polite and friendly. Many offer to help you if it appears that you need help. Don't worry about the language.
2. Both the Tokyo airports have great train connections to the downtown area.
3. Surprisingly, we did not find Japan any more expensive than most European countries. Also, the food is excellent.
4. Don't rent a car, traffic is crowded and you would have to drive on the left. Parking is a special problem.

Here is my writeup of our several days in Japan before our Japan and China cruise, then a cruise that visited ports mainly in Japan as well as China, Okinawa and Taiwan ending in Hong Kong.
Japan and a little bit of China
http://www.cruisecritic.com/memberreviews/memberreview.cfm?EntryID=518503&et_cid=2531924&et_rid=17221689&et_referrer=Boards

Here are some tips. If you want to book tours in Japan, check out Viator.com

Viator will provide tours through local tour companies. The tours we took were named in the link above as well as the actual tour companies if you want to book direct with those companies. However, Viator doesn't add a significant cost on top of the local tour.

Tokyo
Do a city tour that includes the Imperial gardens and more.
Consider going to Nikko north of Tokyo, it was one of the highlights of our visit.
Don't miss going to Kyoto. You need at least two full days there.

If you need more help, send me a message or post again here.

If you provide a few more details, we can give you better answers: what port is your ship using?
What month will you be there?

If you've never been to Japan, please don't plan on renting a car there! The trains and subway are excellent! Taxis are very expensive and the drivers often do not speak English fluently.

Prior to retirement, I was fortunate to travel throughout Japan on business for many years. Get yourself a good Tokyo Subway Map and you can go anywhere on your own (hotels have them or you can print one from the Internet before you travel). However, one suggestion: Maybe take a one-day guided tour with Hato Bus in Tokyo to get the "lay of the land" since the remainder of the time it will be easier to travel underground. You will see some places that you might want to return to on your own - plus the English speaking guide will give you other valuable suggestions. https://www.hatobus.com/

Travel tip: A book which I used on all my trips to Japan is "Tokyo: A Bilingual Atlas" - every map is in English and Japanese! The 1990 version was $14.95 and worth every penny. I also used the "Kyoto/Osaka" version. Even if taxi drivers (or people you encounter) don't speak English, you can point on the map where you want to go and they can show you the way. I'm not sure if this still applies, but the level of English was better in Tokyo than in Osaka. The Japanese people are very polite and go out of their way to help.

I hope you enjoy Japan - it's an amazing destination with wonderful people!

All Japanese study English in school; however, they may not have gotten much practice with spoken communication and may be reluctant to demonstrate their deficiency, real or imagined. A written address or, as another poster suggested, a map with a destination highlighted will help them help you.
I will echo what everyone else has said about driving, DON’T. Not only would you be on the other side of the road, but you won’t be able to read the signs. Tokyo is unimaginably crowded. It would be insanity to drive there even if you were to drive in other parts of the country. Japan is famous for the excellence of its public transportation. However, try to avoid using the metro system at rush hours. You almost have to personally see the crowds to believe it.

We have visited twice. We expected exorbitant prices and were happily disappointed. Particularly we thought food was quite reasonably priced, but we don’t look for high end restaurants anywhere we travel. The resin or plastic models of meals almost ubiquitously displayed in restaurant windows takes a lot of the guesswork out of ordering. Most often we simply walked with the server to the window and pointed. We didn’t find English as widespread as we expected, most especially in Kyoto, but managed very well nonetheless. I suspect the Japanese are more fluent in English than they might indicate but don’t really know. They are excruciatingly polite and helpful- you’ll find your way. A car would be nothing but a liability in my book. Public transportation is excellent. I wouldn’t like to drive in Paris or Rome but would never even consider it in Tokyo. My number one learning experience...learn the formal, not informal form of useful phrases...it made a huge difference. A poster recommended the Hotel Sunroute Plaza Shinjuku in Tokyo and I will do the same. Convenient location near the huge station and friendly helpful staff at the desk. We arrived in Yokohama port and shared a cab to Tokyo; train and bus is available but I have no firsthand experience. Sayonara!

We were surprised how little English is spoken even at hotel front desks. We went all over Japan. There will be someone speaking English in a hotel but not the majority of the staff.
We used Google translate when dealing with Japanese speaking people. Worked great. Enter what you want to say in English, and it changes to Japanese characters. Download English to Japanese before you leave for Japan. Very helpful when using a taxi.
The trains are incredible, always on time. Tickets give train number, car number and seats.
Meals range from simple ramen places that run equal to $10 to an amazing Kaiseki meal at $200. per person. Department stores have incredible food halls on their lower, basement levels. They also offer restaurants on their top floors. Buy a delicious bento box meal for around $10-12.
There is good public transport in Tokyo and well as many taxis available.
I hope you will have enough independent time in Japan in addition to the cruise to experience the people, the culture. It is a beautiful country.
It is also the cleanest place I have ever visited, better than Switzerland. In over two weeks , I never saw one piece of litter anywhere. You are responsible to carry your own garbage, trash including newspapers until you find the rare receptacle.

I agree with what everyone else has said - let me just comment on the Tokyo cruise port.

There is a bus from the nearest subway station to the cruise port, but I'd just take a taxi. The bus runs infrequently; they don't seem to expect a lot of riders. A taxi from your hotel or a nearby subway station is probably the best option.

Hi Pepster,
Just a quick tip to suggest checking whether Japan still offers family stays. They are an extremely rarefied experience not to be missed. Back in the early '90s, the PTP (People to People) program was offered through the Japanese national government plus some banks, and one could stay with local families right across Japan. Dunno whether that arrangement is still possible.
Good luck.
I am done. The end.

As already mentioned, people in Japan speak English but not everybody. However, you will always find someone who will. Even if not, Japanese are extremely polite and will guide you the best way they can to help you get where you need, if they won't be able to explain, they might walk with you.

Yokohama and Tokyo are very close to each other, one train ride will get you there in about 30 minutes.

When it comes to food - you will find many great places to eat. Expensive and cheap - some places have everything explained in Japanese, but many do offer English menus. I would suggest to try them both, for the sake of experience and often the places that have listed everything in just Japanese, might be cheaper but of very high quality. My personal favorite food is Ramen in Japan, and you can find dishes ranging from 6-20 dollars. Doesn't mean 20 dollars would be better than 6 dollars one, all depends on the district and if it's designed for tourists. Here you can find an interesting ramen guide for Tokyo - http://www.sprayedout.com/best-ramen-restaurants-tokyo-japan/. Around Shinjuku in Tokyo, you will find many great restaurants and that's the area you most probably will be in Tokyo as a tourist.

Renting a car in Tokyo? A big no in my opinion. It will cost you a lot and you will waste time as well. Trains are the best forms of transportation, cheap, fast and will get you everywhere in Tokyo. That's how most Japanese people travel there as well.

We stayed in a large Japanese owned hotel. Most at the Front Desk did not speak English but there was always one who did. Concierge spoke English. Traveling around the country we were surprised by how few spoke English.
We used public transit 100% of the time plus a few taxis. Japan’s trains are on time to the minute!
Food costs- You can spend a lot if you order aKaiseki meal, $200 per person or at a Teppan(steak.).
But you can eat at a ramen or udon shop for $10. Yakitori are not expensive either. Department stores have multilevel food halls in their basements where you can buy reasonable foods including Bento Boxes. Lots of Bento Boxes are available for sale in train stations too or at 7-11’s.
I used Google Translate as needed, wonderful.

Most signs in the train and subway stations are in English as well as Japanese. And many of the JR agents at the train offices speak English.

Do not even think of renting a car. They drive on the left, and you may not understand the signs.

Where do you want to go besides Tokyo? Public transportation is excellent, and you will have no trouble navigating. See first paragraph.

As for meals, it depends. Many restaurants specialize in one kind of food. Others offer expensive Kaiseki (chef’s choice) meals that are amazing but expensive ( can be $200 as Suki says). We avoided those and chose local soba or Katsu (fried pork) restaurants, or little p[laces with counter service, where we paid about 1200 to 1900 yen ($11 to $18) and were happy.

You can get a lot of good advice on travel in Japan on TripAdvisor, in the Japan forum. That served us well on our trip last month.

To understand Japanese foods and to get restaurant recommendations buy FOOD SAKE TOKYO by Yukari Sakamoto, wonderful book, slim and packable.

I agree with Suki. Google Translate is your friend. You can translate a few key words and then pantomime the rest. If you are comfortable using a smart phone, you can point the phone's camera at things written in Japanese and get a translation. This technique may be more helpful than simply translating words you type in because you'll need it to decipher things in stores and other places.

I also suggest learning a few Japanese phrases. "Thank you," "hello," and "excuse me." The Japanese have several words that mean similar things, such as ones for "pardon me." I used "sumimasen" a lot. See Sumimasen: The Most Useful Word in the Japanese Language

The Japanese are very helpful, even if they do not speak English. Being polite and friendly goes a long way.

Tokyo Metro (subway) is great, and there are signs in English. Also Google maps will tell you exactly which station and what stops to get on and off at. I spent 5 days there before a cruise, and took the Metro to different neighbourhoods to explore or see particular sites. The food can be very expensive, or very cheap, and everything in between. The high priced restaurants are really high priced, but there are very good meals to be had pretty inexpensively (but it's casual, not fine dining).

My experience was that many people speak a little English, but not a lot of people speak a lot.