Hi Cindy
I was lucky and we were able to do both on the same day on my trip, but if you have to choose, I would recommend the helicopter. It's a brilliant adventure - especially if you are travelling alone because they tend to put the couples in the back and the singles get to ride up with the pilot and have a superb clear view for photos. (It also helped that our pilot was the spitting image of Adam Levine from Maroon 5 but....moving swiftly on....)
The Maid of the Mist is fun but ironically, because of the mist, you won't see much when you are up close to the falls. You get to wear the famous blue ponchos but trust me, you will still get really wet (I suggest taking one of those disposable waterproof camaras rather than risk getting your normal camara wet - that's what I did)
I hope they manage to fix it so that you can do both but either way, you'll have a great day out (don't forget to try the Ice Wine while you are there).
My tour covered most of the places you are going (except Boston) so, if you've got any other questions, happy to help.
Have a super time
Mandy