it's not too late at all. i applied in july for BU's SMP and also Penn's Special Science and I got into both for that september. I think it gets a little iffy the longer you wait since in the past, there's been a waitlist of students wanting to get in but couldn't due to lack of space. Check the websites for this year's deadlines, but when I applied, they were around July 15th.
Also, you should apply to Penn's program a little earlier since their admission process is more involved than BU's. On top of the standard application, recommendations, and standardized test scores, they also require additional essays (I think I wrote a total of 5 or 6 for Penn) and then an interview before they make a decision on you. BU just requirse the standard application, essay, scores, and recs. Their response time seems to vary. Some people end up waiting months, and others hear within days.
Georgetown, I believe, has an earlier deadline (I have terrible memory, but I'm making this assumption because I didn't apply to Georgetown last year, and I'm thinking it must've been because their deadline had passed).