I guided rafts and managed the river operations for Sobek on the Zambezi for 5 seasons a long, long time ago (1991-1995). I kayaked it a few times, but this was long before the river was the kayak mecca it has become now.
Rainy season starts in late November, but really gets cranking around Christmas, and lasts until March or April (memory is a bit foggy). The water starts getting too high for the low-water run (Rapids 1-10) around January or so, and stays high until about the end of July/beginning of August. Trips in June and July (and January, February, and March) will start at Rapid 11, and will miss most of what makes the river so famous. This time is still fun but it is not the classic Slambezi.
I personally prefer (from a rafter's perspective) the beginning of the low-water season (Late July - August), as the river is extremely powerful and pushy, and lines are not very distinct, making for a wild and crazy raft ride. Depending on the year, around October the water is getting very low and rapids become steeper, but the waves are smaller, and the lines are much clearer. Some of the best kayak play spots come out during low water, like Rapid 12B.
Safaris are best during the dry season, which happens to coincide with great boating on the river. Don't miss Hwange in Zimbabwe, or Chobe in Botswana. The Zambezi is awesome but so is the wildlife and you must go on safari, even if just for a day or two.
Regarding crocs and hippos, yes those are not an issue on the day stretch. Crocs become large and more of a problem as you move downstream, and hippos are only really a problem above the Falls or way downstream on the last day of the 7-day trip. Some of my favorite rapids (Upper Moemba, Ghostrider) are downstream of the day trip, but there is lots of flatwater and there are several portages down there. It can be HOT. I'd probably mostly stick to the day trip, or to the dam site, if kayaking, although the camping is fantastic on the lower river. Just remember never to bathe in the river so you don't get eaten.
I would follow other's recommendations and go for a long time - experience the water dropping to see how the river and playability change at different levels. If you can't do that I'd probably go in October to experience the great play at the lower levels. It is HOT that time of year, however, and the water is not super clean when it doesn't have huge flows to spread the sewage out (the Vic Falls hotel dumped raw sewage in the river when I was there - hopefully that doesn't occur anymore).
Sorry my memory is foggy on the details (and thus info is incorrect), but definitely go. Some of the best times of my life were on the Zambezi. . .