You've chosen a great time to visit, Kimberly; fall is my number one choice for time of the year to visit WDW. Having experience with both Disney Cruise Line vacations as well as Walt Disney World Resort vacations, I would say that both offer something unique. That said, personally, I would wait until the two-year-old was a bit older before setting sail. Reason being that the fabulous kids clubs aboard the ships are open to (potty-trained) children ages three and up. At two, your child would be welcome in the nursery area, but there are additional charges for that childcare service whereas the kids clubs are included with your cruise fare.
If you're looking to plan a WDW vacation for the fall, I'd recommend late August through early October as ideal times to travel. As for which resort to call home, unfortunately, the monorail resorts (there are three of them) are not the most affordable places to stay, though they are some of the most convenient, especially for guests traveling with young children. Of the three,
Disney's Contemporary Resort typically is the most economical option. I hope that helps!