I ran the Paine to Pain loop both this past weekend and the weekend before as part of Boston prep, both times after a good rain. And the verdict? The trails have some drainage issues, but not enough to keep a runner off them so long as you don’t mind getting a little dirty.
All of the trails that are part of the official race course are navigable after a good rain. The Leatherstocking has some drainage issues in the New Rochelle section that need attention, but small side tracks generally take you around them. The Mamaroneck section is good.
Saxon Woods is almost all good, though it has two notable mud holes where we want to run the race this year, but nothing terrible and easy to skip around. Twin Lakes and Nature Study Woods have the same problems.
So if you were worried that rain would make the trails impassible, it is an unfounded worry. When the trails are dry, they are magnificent. When wet, merely good. And a hell of a lot better than training on the roads.