If your computer is connected over wifi via ndiswrapper, removing it could certainly cause problems. If you insist on uninstalling ndiswrapper, you may want to disconnect your wireless connection and even remove the windows driver first. If your wifi drops there are many possible causes:
- too far from router
- outdated/unsupported driver
- modem configuration, interference in the building, any other cause that could interfere with wifi...
If your wifi drops, don't remove ndiswrapper. First try to reconnect, what happens? You could use the command
sudo ifconfig [wlan0] [down/up] where
wlan is your wireless adapter (could be wlan1, ra0...). Treat this as a wireless issue and troubleshoot it accordingly. It would help if you would post the chipset and windows driver you're using, that way device-specific troubleshooting steps could be looked at.
See more on wireless troubleshooting here, here, here, and here.