The OP is a URM, so that will help. Without more detail on the EC’s, I think the EC’s are fine. Not everyone is a national (or even state winner) of some academic or artistic contest, or started a company or charity that has made/raised big bucks. It shows a dedicated student athlete. Baseball, hockey and swimming all require a huge time and energy commitment, and in these days of specialization, the three sport varsity athlete is rare. The athletic EC’s would be more impressive if he (assuming gender because of baseball) were a starter all years and won some honors (e.g. All District, All State). Being just a participant is less impressive. Also if he goes to a large school, three sports is more impressive than if he goes to a small school.
OP’s stat’s don’t provide class rank and size to put context to his GPA. Being 5/400 is much different than being 15/125.
All that being said, unless he is a recruited athlete, Yale is a reach no matter what the stat’s or details behind his stat’s and EC’s. What OP can do to enhance his application that is within his control:
- Take the most rigorous set of courses his senior year that his school offers and make A's
- Study hard to get his ACT up a point or more, focusing on the section(s) where he scored the lowest. Try to score in the 700's on 2 SAT2 tests
- Choose his recommenders wisely. They need to be recent teachers who will write more than just superlatives but can and will attach examples to back up the superlatives. Let's face it, many recommenders have templates that they use, especially "popular" teachers who are asked to do multiple recommendations every year.
- Write great essays that shows who he is, tying and making sense of his personality, academic and EC record.
Finally, make sure you have researched and applied to a good range of safety, target and reach schools. Especially look into honors programs in your state’s (or other state’s) flagship universities.