This is a tricky topic, calling for some realistic self-evaluation. You may have the chops to make it into a top 25 school. If so, you could think about one of the smaller PhD factories, or look into the Public Ivies. You can always use the U. S. News and World Report rankings to help you with your search here. If possible, check out the rankings for your particular area of focus.
Letters of recommendation are tricky things.
Obviously, you want to get them from people who like you and who have been impressed with your work. Help out your writers by providing them with your current curriculum vitae. Most professors will make you a copy of the letter they will send before they do so. If it's too lukewarm for your liking, or you feel that she has failed to mention something important, let her know before she sends the letter out. These requests usually processed with great efficiency, but sometimes they can slip through the cracks.