I would disregard the size issue (partly because there's not a lot of difference and partly because DD's school only had an intake of 180 which I thought seemed pretty big!).
Personally I'd focus on;
Do current parents of each school regard the school highly or do there seem to be lots of little issues (haven't heard a bad word about DD's school from parents with older siblings - even episodes of bullying have been dealt with swiftly and effectively whereas everyone avoids another school because of loads of issues)?
Will your child have friends at the school you choose? I know everyone says they make new friends anyway but I think if your child is even slightly shy it helps knowing that for the first few months they can get together with people they know at break/lunchtime/bus home.
Don't underestimate the journey time. I love the fact that DD catches a dedicated school bus literally 100m from our house. She has to leave the house at 7.45 but is home for 4pm. She tends to use the journey to catch up with friends/listen to music/play games on phone.
Because so many kids at DD's school travel by bus, most clubs etc. meet at lunchtime, tends to only be sports matches after school. I agree with a pp, I wouldn't make after school stuff a deciding factor.
Are you likely to get into either/both school/schools? I don't know about your local situation but round here the number of kids in Y6 is enormous and there are going to be loads of kids who don't get a place in their catchment school. DD's head told us at an open evening a few weeks ago that she is dreading admissions this year - in her words it will be 'carnage'. So maybe prepare your DC for either school (or maybe even a 3rd unmentioned one?)
Anyway (after that long essay!), good luck with it all, it was a nightmare for us last year but the people on MN were really lovely and supportive.