East Africa Itinerary

We did a wonderful safari in Kenya and Tanzania in August with Good Earth Tours. The safari was fantastic.
We stayed in a wonderful hotel in the Masai Mara for two nights. It was great.

I will say that we spent more days in Tanzania than Kenya and we saw more wildlife in Tanzania than Kenya.
We did the Serengeti, the N------ Crater and another reserve on our way to Arusha. I suggest checking with Good Earth and go with Tanzania.

We were not interested in Zanzibar since that is more a beach thing, which we can always do in the USA.

If you do the Masai Mara, you will probably have to fly into Nairobi and spend at least one night. However, we saw at a remote airport in the Serengeti smaller aircraft with people flying directly into the safari area. However, our guide told us that tours that include such flights are very expensive.

I have been on safari in Tanzania not Kenya, but news reports in the past few days have been highlighting the severe drought that’s currently affecting Kenyan wildlife with lots of elephants dying and other animal populations including wildebeests and zebra being devastated. It may not be the best time to travel there.

Three nights somewhere is only 2 full days, not 4 days. Your itinerary has a lot of travelling for relatively short timescales on the ground.

We spent 4 nights at a beach resort on Zanzibar, but that was more than enough and we only went there because we were exhausted from climbing Kilimanjaro. I don't think you'll find the beaches or resorts that enticing and the swimming can be dangerous. Stonetown is interesting, but with so much else to see in Tanzania, I wouldn't waste time on Zanzibar....

I'm not sure what flight options from Uganda look like, but we did spend some time in Nairobi before flying into the Mara this past August. I'm not sure I would recommend doing three different countries--that's a lot of travel, visas, entry requirements etc. including different vaccination requirements. I absolutely loved our time in Kenya and in the Mara specifically. It is true that they're experiencing a horrible drought right now; my Maasai friend that I still keep in touch with is really struggling as their cows are dying off. Fingers crossed that is better by next summer.

I am researching East Africa as well, and based on my research, I believe we're going to go with Good Earth Tours, as geovagriffith and others have suggested.
Everyone will have their own opinion of your itinerary, I would present it to whatever company you choose, and get their advice (unless you are planning to do it all independently and take the game drives from each place you stay).
I sent an email to Good Earth Tours on Friday (12/30) late, and received a response already this morning (1/2) even though it hit them over the holiday weekend, so I'm impressed already!
I noted comments about Zanzibar----I think you have a lot of nights there. You may want a beach stay for the kids, but 5 nights might be way too much!

If you do this, keep in mind the East African visa which covers Uganda, Rwanda and Kenya. There were plans to include Tanzania in this but not sure this ever happened. Also, depending on routing, you may be able to get a transit visa for Tanzania rather than the regular visa (this used to be $30 v/s $100 a few years back).

Murchinson falls is great but it will take at least half a day each way getting to and from the park. Also, to maximize time on game drives, make sure your lodgings are not outside the park which eats up your time.

Zanzibar - 5 days seems a lot unless you want to spend most of it at the beaches. Unless you are thinking of 2 days in Stonetown and 3 at the beaches