Thomson drew his conclusion based on his calculation of the charge to mass ratio of the "corpuscular carriers of negative charge in cathode rays". Quoting Thomson's Nobel Lecture of 1906:
This constant value, when we measure $e/m$ in the c.g.s. system of magnetic units, is equal to about $1.7\times10^7$. If we compare this with the value of the ratio of the mass to the charge of electricity carried by any system previously known, we find that it is of quite a different order of magnitude. Before the cathode rays were investigated, the charged atom of hydrogen met with in the electrolysis of liquids was the system which had the greatest known value of $e/m$, and in this case the value is only $10^4$, hence for the corpuscle in the cathode rays the value of $e/m$ is $1700$ times the value for the corresponding quantity for the charged hydrogen atom. This discrepancy must arise in one or other of two ways; either the mass of the corpuscle must be very small compared with that of the atom of hydrogen, which until quite recently was the smallest mass recognized in physics, or else the charge on the corpuscle must be very much greater than that on the hydrogen atom. Now it has been shown by a method which I shall shortly describe, that the electric charge is practically the same in the two cases; hence we are driven to the conclusion that the mass of the corpuscle is only about $1/1700$ of that of the hydrogen atom. Thus the atom is not the ultimate limit to the subdivision of matter; we may go further and get to the corpuscle, and at this stage the corpuscle is the same from whatever source it may be derived.
See the linked transcript for details of Thomson's method of calculation.