In terms of a high ranking university based in the centre an old, smallish city, Durham is probably your best bet in England (although scientists will spend the majority of time 'on the hill' to the South of the city centre). In Scotland you have St Andrew's and maybe Edinburgh if you stretch your definition of small.
There are plenty of good* Universities in historic towns (e.g. Bath, Exeter, Kent, Lancaster, York, Surrey, Stirling), but these are mainly plate-glass Universities on campuses on the outskirts (or even a short distance away). Most RG Universities are in or near the centres of larger regional cities and London for historic reasons.
Bear in mind that that, while pretty buildings are nice to have, their presence or absence is unlikely to be the defining element of your time at university.
(*Good is obviously a matter of opinion)