ACfan... I have been to both places. I would have to say that I enjoyed Tikal the most. Tropic Air offers both day trips and overnite (staying in Flores). Check out their web site for tours... http://www.tropicair.com/tours.html
I did the overnite and thoroughly enjoyed the whole adventure. I would highly recommend it. I plan to revisit Tikal to do more exploring. Check out the message board here under search, as I believe others have spoken highly of the site. You might want to pick up some advance reading material on the ruins before you go.
I also loved Flores with it's quaint shops, the market, the layout of the streets, the churches, etc.
Whatever you /they decide ENJOY!