Fallsview Waterpark

Fallsview has a better waterpark but the hotel part is not as nice as GW. If you are there for the park and not too fussy about accommodations, then go for it.
 
GW is a much better overall experience with the themed rooms and the lockers and wristband keys. There are always specials available but it is pricey.

Fallsview isn't bad and you have a choice of various hotels you can stay at. You also have the casino right there if interested not to mention Clifton Hills.

Both are great.
 
I took my son to Fallsview on a weekday, and it was he, I and four other people. So no waiting for anything what so ever. We first went to Great Wolf, but they only allow you in the water park if you get a room. For a day visit, Fallsview is good.
 
I go to both, but if the price were the same, I would choose GWL. I think GWL is better for smaller kids (under 42") as there are more areas. Fallsview allows 42" alone on their tube rides but at GWL they need to ride with another person. Overall, I think Fallsview has more slides for the adults (2 non-tubes and 2 mats), but it doesn't have the lazy river.
As dragnbiz said, the lockers are a plus for GWL and since I usually stay at the Hampton (for the lowest rates and breakfast), we need to walk through the casino parking lot.
Fallsview has the benefit that you can get food from any restaurant you want, at GWL, I find we eat onsite (not required, but who wants to load into a car and drive after swimming all day) and it is poor and expensive (esp. dinner).