Thanks everyone - still interested in more responses if anyone has any, especially from those with DCs at Crypt. Despite all the strong recommendations for Tommies, my gut is still saying Crypt would be better for DS. The main factors are:
1) As a shy and introverted boy (who is nevertheless a lot of fun when you get to know him) I feel he might be more comfortable in a mixed environment. He's part of a close group of 4 at present, one of whom is a girl (they will sadly all go different ways at secondary school). He's into his games consoles (but prefers playing online with his friends to playing alone - he's not a loner) and enjoys puzzles. I find it hard to imagine him growing up without girls around him (although he does have a sister) - he is not outgoing so he's not likely to meet them in extra-curricular activities.
2) He's competitive academically and very hard on himself when he perceives he has failed. He's joint top in his class at school and likes that. The place he went for his 11+ tuition had him working on Year 7 maths because he got through the Year 6 maths so quickly, and he thrived on the challenge. Conversely, although he's patient when helping others, he also gets frustrated that not everyone is as clever as he is! He's been looking forward to being in a more academically challenging school environment (Year 6 is boring!). I think he would get that with both schools but.......
3) At Tommies he would be with a lot of other children of a similar standard (probably lots of others who were hoping for Pates). How would he feel if he were no longer close to the top? Although, who's to say he wouldn't be? We don't know his exact score but he was in the Top 150 for Tommies, Marling and Crypt (the latter being harder because it's mixed) and he only narrowly missed out on Pates at 235. We had that discussion when he was hoping for Pates, and he understood that everyone else would be very clever too. He wanted Pates enough because it was so convenient to get to for that to outweigh other considerations.
4) Conversely, at Crypt there will be more variation in ability - but everyone is still going to be good, otherwise they wouldn't have got in! At Crypt I would expect him to be nearer the top of the class, at least for some subjects, which he will like and will boost his confidence. They also have a gifted and talented program. I have no idea whether he would fall into this category but I like the idea that if he did, they would stretch him.
5) Convenience - it's the same bus stop for both and he can go with his sister, who's at Ribston. If he goes to Crypt it's the same bus but they are only minutes apart so it's not a major consideration. Crypt is further for us when we have to go but we already do it for our daughter.
6) Sports are not a big part of his life. He does like basketball, but has never put himself forward for team sports because he doesn't like to push himself out of his comfort zone. He hates the idea of rugby! I know rugby is a big thing at Tommies - and I know that not everyone plays but it does seem to be the default (based on what I've read here).
7) Tommies seems quite formal and old-fashioned. I picked up on Glos18's comment about it being strict. DS is very sensitive. If you tell him off or (God forbid!) shout at him, he retreats into himself. He may have a good reason for whatever he's been told off for, but he would never tell the teacher, he just takes it and goes quiet. To thrive, he needs an environment where teachers are patient and gentle with him. Telling him off is fine and necessary sometimes - but he doesn't have the thick skin that some other children have. He is definitely not an Alpha male! This is something I hope he will learn to cope better with as he gets older. But I've heard that Tommies are very good pastorally - what about Crypt? Fairypig's DS has obviously had a good experience.

Fairypig's post about her DS' experience of Year 7 in Crypt was really encouraging. If DS were to come out of his shell enough to sign up for a club, I can see board games, chess and raspberry pi in particular being right up his street! I also like the idea of the school challenging his own perceptions of himself. His self-confidence was a real problem right up to Year 5 (because he is so hard on himself) and his 11+ tutors worked hard to build him up. Once he started to believe in himself, he started to fly! This is what he needs from a school in general, I think - a lot of encouragement and not just academically.
I can't comment on the attitude of Crypt's rugby team although I take the point being made. Obviously I completely agree that this is unacceptable behaviour but I don't want to make my decision based on that!
We're going to the Open Day - it's a year since our last visit, although DS went in July for the taster day (which he liked so much that he said he wanted to go there if he didn't get into Pates). The last Open Day was very busy and hectic - so many people! I'm hoping we all get a good feeling from this one as I just want to know that I am doing the right thing by turning down a guaranteed place at Tommies for Crypt.