Moscow tour options

I'd probably vote against a full-blown river cruise between Moscow and SPB; I think it's educational and convenient, but not extremely picturesque (for the most part) and you generally could make a much better use of your time if you do a land tour instead.

You also might want to consider a DIY approach - both cities are quite tourist-friendly, and, with your visa taken care of, you get the most frustrating part out of the way. I'm sure some people on these boards will be happy to help you with a diy itinerary, but they will probably need some info from you to get an idea of your interests, timeframe, etc.

If you do like river cruises, though, you might also consider a "weekend cruise" say, from Moscow to Uglich and back, or from SPB to Kizhi, from a Russian provider.

PS. There is a recent thread along similar lines from @hopeperry.

I havn't taken a cruise from St. Petersburg to Moscow, so I can't comment directly on that. I have taken both the day train (Sapsan) and the fancy sleeper train between these cities. Both were very good experiences, and I'd recommend either one, depending on which works better with your schedule. Don't fly between the cities; avoiding the airport hassles is particularly useful here.

Agree on the high speed Sapsan train, took 3-4 hours total and was very easy. No particular enjoyable scenery though. If we had driven could have seen some stuff around the Golden Circle, but we never considered it. And not that you asked, but Uber’s were plentiful in both cities.

(not that anyone asked, but I love Uber and other rideshare services, so...)
As of today, you will need to install a separate, Russia-specific Uber app. The global one doesn't work in Russia any more (and the Russian one doesn't work here in the US), which, in my opinion, effectively nullifies the only competitive advantage Uber has had over Yandex, Gett, and other, smaller rideshare companies.

Several years ago six of us took tours of St.Petersburg, Moscow and 14 days river cruise on Volga from Moscow to Astrakhan. I can recommend this travel company: http://www.expresstorussia.com

We did a wonderful tour of Ukraine, Russia and the Baltic countries in 2011. It included a 7 day river cruise from Moscow to SPB. The cruise was great. We learned it was built under Stalin and 1.3 million people died building the canals.

Going Do it Yourself in Russia is not for the faint hearted. Just taking the METRO in Moscow unless you can read the cyrillic language you will have no idea what station is what. Also, some areas of Moscow can be dangerous, especially at night.

The company that did our tour doesn't do Russian River anymore. You need to do some research. There are still companies that do the cruise.

Just taking the METRO in Moscow unless you can read the cyrillic language you will have no idea what station is what.

Might have been the case back in 2011.
As of last summer:
All metro maps have station names displayed both in Russian and in English (smaller, less readable font).
All newer trains (which pretty much means all lines except the green one) have a marquee display showing the the next station, in both Russian and English, as well as, in some trains, a large LCD touchscreen with English-language option.
All pre-recorded voice announcements within the circle line are also in two languages.

For greater peace of mind, one might want to install Yandex Metro app, in English, which calculates best routes and times in transit, and shows you which metro car you want to board to save time on transfers. Google maps (public transit option) can do it, too, but with far fewer bells and whistles.

I would say if you want to travel in Russia independently learn at least cyrillic and even better some basic Russian. I can communicate in Russian (not fluently) and it made for our group of six tremendous difference. There are not many countries where lower percentage of people speak English. And they have English as a mandatory language since first grade. They did not have anything in English in Moscow metro in 2012 when we were there. St.Petersburg had many signs in English for tourists, Moscow nothing, not to mention other towns, we saw about 14 towns on our way from Moscow to Astrakhan (2600 km) on Volga river cruise run by Russian company - the only English speaker was our guide as she called herself Olga from Volga. For me the most memorable was Volgograd - former Stalingrad where the largest battle of WWII happened and the Nazis suffered the first great defeat. Many memorials around there including impressive Mother Russia.

We’ve been to Moscow twice and used Dan Petrov both times. Funny, witty, extremely intelligent, dependable and just downright friendly. He was really quite affordable and every day with us seeing and doing whatever we wanted. I highly highly recommend him.