I think the thing about a Nile cruise is that you would actually be quite well insulated from potential problems. The Egyptian authorities seemed very clued up about protecting tourist sites when dh and I did a nile cruise for my 40th.
I would do it again in a heartbeat - we loved it, and saw some amazing sights. It is hard on the feet, as you walk round so many temples, but the guides are very knowlegeable and you forget minor aching feet listening to them.
One thing you need to know - and that is the egyptian for 'No thankyou' - "La Shokran" - you will use it all the time as every tourist site has lots of merchants trying to sell you stuff. You'll even need it at baggage reclaim - there are men standing inside the curve of the baggage belt and when they see you spot your case, they grab it for you (helpfully?) and expect a tip from you for taking it off the belt!
Also you have to buy sheets of loo rolls from a lady at the door of the loos at tourist sites (I knew about this ahead of time, and took lots of packs of tissues to put in my handbag, so I could avoid this).
When we came back, there was no weighing of luggage - we had packed carefully, and were pretty sure that, despite buying a 2 foot tall Anubis statue, we were still within our allowances - but at Luxor airport the baggage scales were just somewhere for bags to be put whilst transfering them to the baggage handling side - we saw two lots of bags on there together!!
I would definitely recommend the nile cruise - and in June it will be beautifully hot - so choose a boat with a plunge pool on the top deck.