If the computer has a line-input, I'd use that. Mic inputs are notoriously noisy when connected to the wrong signal source. They're often 3-terminal ports where one contact sends a small DC voltage to power the electret mic itself.
Your cable used to go from the scanner to the isolation transformer matters too as does the one from the isolation transformer to the mic input.
The scanner usually has a monaural audio signal. However many newer scanners have a stereo audio jack which allows use of a set of Walkman-style headphones or earbuds. The audio is still monaural; just fed to both speakers. This can cause problems.
I suggest using a monaural 3.5mm shielded cable plugged into the scanner. This shorts the ring terminal to ground where it contacts the 'extra' terminal in the scanner that feeds the second headphone's speaker. You only need to be dealing with 1 signal at a time. Don't worry - the scanner is designed for this type of connection and won't be damaged.
Connect the tip and shield to one channel of the ground loop isolation transformer. These are commonly sold with two transformers in them for use with stereo signals. You only need one.
Take the appropriate output and, using a monaural shielded audio cable, connect it to the Line-In jack on your PC using either one or both channels. You may have to solder up your own connector or use an appropriate adapter but use the Line-In and not the Mic-In whenever possible.
If you must use the Mic-In jack, you should make sure you DO use a stereo type plug but you also must make sure to only use the TIP and the SHIELD and not the RING terminal.
Another helpful device is an adjustable audio attenuator in-line between the isolation transformer and audio input jack. This reduces the audio level to the range the Mic jack was designed for.
Install a VU-Meter application on the PC and use it to fine-tune your audio card's RECORD SETTINGS. You may have to dig around to find these, but they're the ones you're interested in adjusting, not the PLAYBACK SETTINGS.
Set the scanner's volume and PC's record settings to a point where the loudest sounds will be just below the 0 dB overload area on the VU meter application. I've found this gives the best range of audio without adding noise. The idea is to have somewhere around 50% volume on the scanner and then reduce it with the record settings so that you eliminate most outside noises by lowering the noise floor. For example, if you have the volume on the scanner at 1 and the mic input all the way up, the audio is susceptible to any noises or buzzing from AC sources. However, if you have the volume on the scanner at 5 and the mic input 1/2 way up it takes a lot more noise to overcome the louder audio input.
This works both ways, however. Don't turn the scanner all the way up or you may get into the area where the audio amplifier begins clipping and distorts the audio.