Bedlam is the place I feel most comfortable spending time in. Annie's is the place to dig for gems. Root & Press is small but well-curated. Your wife will be finished browsing in like 5 minutes tho, and personally I think their food is overpriced for the quality. Tidepool feels too sterile for a bookstore.

Overall suggestion is go to Bedlam on a weekend morning and then head over to Birchtree for brunch and discuss your book choices.