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.