Well, I think Thomson knew of the existence of the electron and I think it was a known fact for a certain time.
The great idea of Thomson was to measure some properties of the electron.
It was like to know of the existence of a planet (because its gravitational interference on other objects) without actually having seen it...you can deduce a lot of things about it!
Thomson deduced the ratio between the charge and mass of the electron (quite a wonderful achievement!!!) using a brilliant experiment and equally brilliant reasoning.