Shari, I agree with Charming that you'll very likely see some fall colors, even though peak season will be later than usual this year. Your best chance is further north than where I am located -- Bar Harbor and into Canada. It won't look like what you might see in the brochures, but I'm sure you'll find it pretty nonetheless.
For what it's worth, I would have picked the last week in September/early October for a New England cruise myself. Any earlier, you'd miss the chance for fall colors completely, and any later and the weather might be too cold. (We saw snow in Newfoundland in October 1999.) As you said, the peak season itself is unpredictable so far in advance. I hope that makes you feel better. And, I know you'll enjoy your cruise!