How to disable built-in Wi-Fi and use only USB Wi-Fi card?

Add the following line to /etc/network/interfaces:

iface wlan0 inet manual

NetworkManager doesn't manage interfaces configured in the interfaces file. Replace wlan0 with the interface you want to disable, if it's not the name of the built-in interface.

Then restart network manager:

sudo service network-manager restart

I think the easiest way to do this is with ifconfig.
EDIT 2021-03-02: Apparently, if you're still using ifconfig you're living in the past, so have a look at Gabriel's answer below for an ip solution. Read below for the old ifconfig solution.

ifconfig solution:
Run

ifconfig

then look at which adapter you want to turn off, in my case wlan1 is my internal wifi and wlan2 is my usb wifi. Then run

sudo ifconfig wlan1 down

and it will turn off (type ifconfig to check, note that in the network manager the adapter still shows, but it is turned off). To turn it on again:

sudo ifconfig wlan1 up

and that's it.

To blacklist the module of your wireless card:

1. sudo vi /etc/modprobe.d/blacklist.conf (or create a custom one)

2. Uncomment the module name that has a # in the beginning of the line:

   blacklist eth1394
   

3. Save, run sudo update-initramfs -u and reboot

To remove a module manually without rebooting:

sudo modprobe -r eth1394

Looses effect after reboot.

To load the module:

sudo modprobe eth1394

To see modules loaded:

sudo lsmod

Connect the USB Wi-Fi dongle and disable the internal Wi-Fi adapter as below:

1. Identify your adapter's name by:

   ip link | grep wl` or `ifconfig | grep wl
   

   The adapter's name should be something similar to wlp2s0 or wlan0, in which the digits in the names could be any number in your case.

2. Disable the adapter by:

   sudo ip link set wlp2s0 down
   

   or:

   sudo ifconfig wlan0 down
   

   In your case replace the adapter's name respectively.

This will ensure that only the USB Wi-Fi adapter is active even though the internal Wi-Fi driver will still be active.

ALTERNATIVELY

Disable the internal Wi-Fi driver module:

sudo modprobe -r iwlmvm

This will ensure that only the USB Wi-Fi dongle is active.