maybe it needs a dedicated hot & ground directly from battery, or at least not grounded to anything but battery.just a guess. most people just hook all the hots togather & all the grounds togather under the console & call it good. I'm rewiring a boat I just bought.man what a nightmare!! I ran a 8 gauge positive & a 10 gauge ground from the battery to a terminal strip under the console. am running all positive wires to one side & all ground wires to the other. that way I have dedicated lines straight from battery for each. I bet your ground is tied in to other grounds which are tied in to the motor ground. hence motor noise.
If it is an "economical" radio, probably not much you can do but replace it. Ignition noise is "AM-like" in its nature and a FM radio should be pretty immune to it.