"Three or four hours from Heathrow" (presumably flying from North America) puts you over the N Atlantic, NW of Ireland on the Great Circle Route. The ocean there is over two miles deep, even if you were over fabled Atlantis itself, you wouldn't have been able to see it through that much water. The North Atlantic basin has been very thoroughly surveyed and mapped too, for both submarine navigation and for geological studies of the mid-Atlantic Ridge.

I presume again (your account is short of details) that you were in a commercial jet airliner. That far from the UK, you would have been flying about 6 miles above the surface of the water. Even a big city miraculously floating at sea level would have shown very little detail that high up. Big skyscrapers, maybe; certainly not houses and streets.

Unusual cloud formations? Contrails? Anomalous seismic standing waves interfering with each other and exaggerated by low-sun shadows (what time of year was it?)? A very unusual inversion mirage? Or perhaps a false memory or even a dream? (Don't be insulted, I've experienced, and verified a couple of these myself, it can happen to anyone.) These may seem unsatisfactory explanations to you, but they're all more plausible than a city in the sea.