They just implemented this function:
https://github.com/Microsoft/vscode/pull/3495
You will have the user settings externalTerminal.windowsExec and externalTerminal.linuxExec , where you can determine which console emulator to use.
In my case, I am in windows using conEmu. My user settings (settings.json) are configured as follows:
{ "externalTerminal.windowsExec": "conEmu64.exe" }
EDIT: It is already available in a stable version.
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