Three months isn't long enough for your PI to get to know you well enough for a really solid LOR, in most cases. But you have no choice, as there is a general expectation that you'll provide a letter from whomever supervised your research activity. You should probably make a point of chitchatting with this person often, asking good questions, etc. so the PI has the best chance of knowing you as well as can be, gets a sense of how your mind works and your work ethic, and is well aware of your career goals