So I just got my tascam 1641 to replace my line 6 toneport gx. I was thinking about trying to micing my guitar and bass amps but they are so noisy

If I plug the bass/guitar directly into the Tascam 1641 the signal is noise free (if I have the tone knob turned all the way down, as soon as it goes up it gets very noisy) but there is no tone... It is just a straight signal.

With the tone port I had all those different amps available to me, is there any programs like the line 6 (gearbox) software that will allow me to get a tone with my instruments?

Or should I just stick with the tone port for recording the bass and guitar?
so exactly what are you doing? are you micing the amps or running them direct? guitar rig is another amp simulator that you could use insted of line 6 toneport.

and its a personal preference, the gearbox will make your instruments sound synthetic and weak while real micing on a good amp will make it sound heavy and full. yes you can accomplish that sound with an amp simulator, but it takes a while and if you dont have common knowledge how to use it then it will take some time and make you frustrated.