Yea, first thing, ditch that glass mount antenna. They don't even work as well as a walkie talkie'* antenna.
Second, look for some LM-20RF filters. They're anywhere between $10-15 each. It'* most likely the fuel pump causing most of the noise. Even my WJ is noticible. The bronco was bad until I put two of those in.
You have to connect two of them, one inline in the power, one inline in the ground, to the fuel pump, and then ground the tabs of the filters to the chassis/body. That'll cut a lot of it right there.
Personally, I have no quams about drilling a hole in my roof for an antenna... as long as it'* a Wilson. The mounts are sturdy, and will outlast the vehicle. Plus, I never trade-in my vehicles anyway.
Holes for trim, holes for lights, holes for factory antenna, what'* one more?
But, yea, on the cheap, you can get a Wilson Lil Wil mag mount antenna. The SWR can be tuned well, to get it below 1.5:1 on all 40 channels, and they're the best antenna of their size (about 3' tall), base loaded steel whip.
You can try putting a filter on the power leads of the radio, too (one from radio shack, or walmart, or wherever will work), but most of the noise is picked up thru the antenna with the RF signals, not thru the 12v power.
More expensive radios may have better filters, and some even include them in-line with the power cord. Usually only seen on Ham (or "export") radios.