Maths and sciences at A-level are hard, if he wants to carry on with them, then he should be aiming for at least a 7 in maths and 6s in the sciences, but ideally higher.
If he's not on track for this, I'd suggest looking at something like btec applied science at a college - it's still a great route to uni and suitable for many degrees. He is much better off getting distinctions from a btec than D/E grades at A-level.
If he wants to do a science degree then at least 2 sciences (they will include maths) are needed. Maths will open lots of doors to degrees like engineering etc as well.
In terms of school Vs college, if he's happy in school I probably wouldn't bother. However, for sciences, they may have better facilities, and for something like physics, in a school sixth form you need to be confident there are enough physics teachers especially - what happens if one is sick etc?
In a college, there will likely be more specialist physics teachers so that the class can be protected a bit more (this does depend on the size of the college, though).
He also may just be ready for a change at 16 and it can be a good transition between school and uni, and there may be more extra curricular on offer for sixth formers.
If you're at all unsure, you can apply to both and make a decision later on.