There is seafood everywhere in Portland and on any of those stops, it just depends on how much time you have at the ports of call. Also, it is a little off season to take advantage of the many great outdoor "lobstah" venues and some close after Labor Day. Portland Lobster Company is located in the Old Port on Commercial St on the water and offers all the usual with local beers on tap. DiMillo's has a floating restaurant on Commercial Street with full menus but is a little more expensive based on location. I'm sure that you will get lots of input from others that have been to the same ports as you and in early October.
We have been on the Explorer and its a great ship. Enjoy!