T.D.
I would suggest Great Wolf Lodge in either the Poconos or Niagra Falls. The Falls will be a farther drive ( about 5-6 hours) ,but there is tons to do around there. The Poconos also offers a great choice and is much closer. The Lodge has Family Suites that have a separate room for the kids. As a TA for nearly 8 years, I get requests like this all the time. The lodge has an amazing indoor pool with something for everyone. Even if the weather is not so good outside, you can use the pool inside. They have an outdoor pool in the Summer too. There are some great restaurants int eh area and outlets for some shopping for Mom. Your son is a little young for rating but when he gets a few years older, there is easy rafting in the area too.
Just my two cents.
T.