My two boys have been at Thomas's Clapham all the way through (younger one now in yr 6) and we are very happy with the school. Lovely atmosphere, great teachers and inspiration, lots of parental involvement if you choose to take it up.
Both good schools; I think the main differences are in the first few years and then in the prep years as you've already noted. Thomas's has the Reception year when the kids are slightly separate in lovely purpose-built blocks, but then they go into the busy main school. Broomwood has longer in a quieter environment because of the different school buildings (as I understand).
So I think you should look at the personalities of your boys and how they have coped with nursery. Historically Thomas's has tended to suit the more confident children (and the more boisterous of the boys) who are energised and stimulated by lots going on around them, and Broomwood to suit the more nervous children who might feel a bit intimidated by the numbers and do better in a smaller scale - big generalisation, I'm sure. Obviously both schools have already offered your eldest a place, so they think he would be ok in their environments - but you will have a bit more of a feel for what would bring out the best in him. Is he extrovert or introvert, chatty or quiet, old for the year or young? And does he have any opinions on this (my eldest proclaimed loudly and confidently on exiting his Thomas's interview that it was the school he was 'going to go to'!)
Another direct point of comparison I'm aware of. A friend of mine moved her daughter from Thomas's to Broomwood in year 5, as she had started to struggle to keep up academically and, although the school were doing what they could to help, she was losing confidence. She has settled in very easily and found that the work there moves at a slower pace so she has been able to keep up fine. Both schools obviously get to a similar academic point by the end of yr 8, so it probably comes down to Thomas's going faster earlier because of all the children needing to do exams in yr 6 for day schools, pre-tests etc. Incidentally her son in the year below has remained at Thomas's and thrives, so it really is a question of matching children to the most appropriate school.