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With very small kids the cruise boats may not be such a good option: The staff will certainly be nice, but the rooms are small, there is no play area, and the boats are not really made for kids (staircases, lots of rails where children could fall off…). Occasionally there are kid's programmes on the ships, e.g. on the MS Mahrousa, but I think they are meant for somewhat older kids. Most of the guests are older people, and the sightseeing tends to be boring for children.
If you do want to go, it is usually cheaper to book those cruises from abroad, so don't count on a good last-minute price on the spot. (Also, you get more customer support if you book with the big Western tour operators, and refunds if something should go wrong)
You could consider a felucca trip instead, ideally in Aswan. Then you can have the whole boat for yourselves, bring snacks and do what you like.
Photos, hotel reports and texts from our Egypt trips: http://westwards.typepad.com/westwards/egypt/