I haven’t worked with an independent publisher in fifteen years (not that I’m opposed). But I have lots of writing friends, as well as students, who are considering working with independent publishers asking me about contracts. Now I don’t have the best natural brain for business so this is not my area of strength. However, off the top of my head, here are questions I would ask:
1. I would definitely find out about their distribution channels. Do the go through Ingram’s or another distributor for hard copies? Do they have a book rep reaching out to independents?
2. Do they submit to Amazon, IndieBound, Barnes and Noble, or other online retailers?
3. Do they attend ALA, Book Expo and other important trade shows?
4. Do they submit the book to reviewers and especially bloggers or is that something you will need to do yourself?
5. Will you be able to buy the books at a discount?
6. Do they get an ISBN for you and register with the Library of Congress?
7. Will you retain the copyright??
8. If the book goes out of print or the publisher goes belly up do you have the right to publish it again?
I would would also look into joining the Author’s Guild and get free help from their legal department as they will typically look over contracts for you. I hope this helps. If anyone has other suggestions, please add your two cents!