The Musai's Anti-Air Missile Launchers

[MythSearcher]

I'd say laser guidance is a more preferred choice, considering Kuniowara specifically designed a laser guided spy missile that has a control range of 200km.
IR is possible after inertial guidance once close enough like Seta Kaiba said, diffraction makes it harder than normal but if you are at the proximity, I guess IR doesn't have the range to diffract too much and you still get some sort of accuracy out of it.
However, active radar likely has a lot of problems even at close range because of M particles being more dense around their scattering point and can be completely blocked.

Come to think of it, maybe visual detection and motion sensing can be used as well, in a lot of cases we see MS and ships being id-ed on screen thus computers can pick out these things from the background, which can also be used for guidance data.