I was in similar position to you several years ago. I'm in Stokey, just around the corner from Stoke Newington HS. My DD ended up going to St. Marylebone, and I'm very glad she did (as is she). We never considered Clapton, as we were too far out of catchment.
Academically, there's no comparison - St. M is miles ahead of Stokey, but they aren't a hothouse, iykwim. St. M has excellent pastoral care as well. Basically, St. M sets very high standards of work and behaviour, without being quite so regimented as Mossbourne (no disrespect to Mossbourne - I know some kids there really thrive).
Stokey has a bad history of tolerating sexual harassment. I know personally of at least three girls who transferred out of Stokey in one year after incidents. I wouldn't send a girl there, unless she was incredibly psychologically and physically tough. Even then, why should a 14 year old deal with comments about her body on the way to Chemistry?
Another upside to St. M is that it is far more mixed - racially, culturally, economically than Stokey. Her friends come from all over London and aren't just children of white Hackney creatives (and I'm a white Hackney creative!).
About the commute - this was my biggest worry, but actually, it's been fine. DD uses the commute (obviously no commuting lately) to chat with friends, decompress, and sometimes study. Because the upside is that she's become incredibly independent, travelling around London by tube and bus and overground. She LOVES giving tourists directions.
Feel free to message me if you'd like any further info.