I'd leave the tops on until next Spring's cleanup. The dead top-growth will help protect the crowns.

Basil won't overwinter in zone 5. Go ahead and cut that right down. Heck, basil won't over autumn here. Once it gets to 45 or so at night, there goes basil. Ditto Lemon Verbena. however, you might try bringing in the lemon verbena as a houseplant. The chamomile will self sow abundantly, so go ahead and harvest what you want. The peppermint, spearmint and catnip are perennials in zone 5. Harvest, leaving an inch or two of the plant. They die back to the roots anyway. Next spring, they will send up new growth.

With perennials I harvest until they begin to look too ratsy (the the plants will say when they are giving up for the season) or the killing frost stops them. Keep an eye on your local weather reports for frost warnings.

Since I like winter interest in the garden beds, I do not clip and clean up my gardens in the fall. Who wants to look at empty dirt or undinted snow all winter? I like to leave the dry and dead plant parts until spring. Here's some snowy pictures to make you think of what your winter time garden can offer:

Queen Anne's Lace

Elecampane

When snow and ice coat the remnants of last season's plants....it's magical. Echinacea cones, teasel seed heads, and even the simple ones like lemon balm and oregano are quite pretty and reminders of greener, warmer times.

FataMorgana

Thanks everyone! As for the lemon verbena, should I still cut it down to a few inches, if I bring it in as a houseplant? I think the leaves will die anyway inside, and I wouldn't want to waste them. Or instead of cutting down would I just pick the leaves?

Beautiful pictures by the way!