My personal take - I would not accelerate your son. Even at a high school with limited advanced course options, you want to take a variety of courses and make sure you have a solid foundation in math.
When he applies to colleges, they will be aware that your HS does not offer AP science courses, so that should not count against him. Perhaps he could take a more advanced science course over a summer, though I have no idea what options you have. Around us, the community colleges are not as rigorous as many of the high schools. Our public HS will not accept science courses from the community college, though they will accept them from area private schools.
I get the sense that there aren't many advanced students at your high school. Our public HS, which my kids attended, offers Multivariable Calc and Linear Algebra, so the "regular" kids don't need to look outside the HS. My older two both had kids in their class that had finished all the HS math classes by end of 8th grade, so they went to a local college for math - we are fortunate to have three four-year colleges within a mile of the HS (and another three within three miles).
My middle kid was my most advanced in math, and she wasn't super advanced - took Linear Algebra senior year. She also explored the other subjects and opportunities that HS has to offer. She took two foreign languages through AP level, played two varsity sports (played one on a year round travel team as well), had a part-time job and served as a student rep on the board of a local educational non-profit. She also participated in the typical stuff, like prom and pep rallies. She enjoyed her HS years.
She went on to a good college, though not elite - she did not get into any of those. A profile like hers, with good test scores (NMF, nine 5s on APs), doesn't mean much in the age of holistic admissions. She is now in a very good PhD program in her chosen field. And one of her undergrad degrees was Applied Math.
Long story short, I wouldn't rush things. Of course, just my opinion - wish you luck with whatever decision you make.