There are two main arguments for a corpuscular view of light:
(1) Light consists of rays of inherent and inalterable dispositions (as regards colour, refrangibility, etc.). This is argued for throughout, but see esp. the classic prism experiments in props. I and II. Wave theorists, on the contrary, base their explanations on modifications of rays.
(2) The law of refraction "may be demonstrated upon this Supposition. That Bodies refract Light by acting upon its Rays in Lines perpendicular to their Surfaces" (p. 79). Consider what happens as the ray passes through the strip from y=c to the surface boundary at y=0. Newton states the lemma that the vertical velocity v_2 at y=0 will be determined by the initial vertical velocity v_1 at y=c and the would-be vertical velocity v_0 at y=0 if v_1 had been 0, as follows: v_2^2=v_1^2+v_0^2. Newton omits the proof as being too easy; it may be supplied as follows. Think of the v's as functions of y and differentiate. Both sides vill be of the form 2v(dv/dy) = 2(dy/dt)(dv/dy) = 2(dv/dt) = 2a = proportional to F, which is equal at equal y's. Thus since the lemma holds for c=0 and the derivatives are equal it holds generally. Though Newton emphasises that he has not assumed anything about the nature of light, we see that this proof makes most sense from a corpuscular point of view since it in effect appeals to F=ma. A further side effect of this proof is that it implies that light speeds up when it is refracted towards the normal, which implies that light is slowest in vacuum and fastest in dense materials.
(1) and (2) are elegantly combined if rays of different colours consist of particles of different sizes.
Further arguments against the wave theory (Query 28): light does not "bend into the Shadow"; it cannot explain "the unusual Refraction of Island Crystal"; it needs two aethers to explain the "fits" in the next paragraph; "against filling the Heavens with fluid Mediums, unless they be exceedingly rare, a great Objection arises from the regular and very lasting Motions of the Planets ... for thence it is manifest, that the Heavens are void of all sensible Resistance."
Nevertheless, waves are needed to explain interference patterns and the fact that light is in alternating "fits of easy Reflexion and easy Transmission" (p. 281). This can be done as follows (Query 18). When light goes from one medium to another it strikes the aether, creating waves like ripples on a pond. These ripples travel faster than the rays and "by endeavouring to expand itself" (p. 352) the aether is thus alternately pushing and pulling on the rays, causing the fits. The existence on the aether is suggested by the fact that thermometers behave the same in vacuum as in air (Query 18). Since light and heat are capable of generating each other (Queries 8-10), it is plausible that this aether is the same as that of light.
The other major theme in the book is colour theory. This is all very good, but it is not very exciting since these ideas are so commonplace today. An interesting exception is Query 14 where it is suggested that harmonious colour combinations are due to harmonious combinations of frequencies, as in music.