I use QNX 6.3 on a 32 Bit Pentium and usually configure works (at least to some state beyond guessing the host system). There is a script calles config.guess which determines your host machine type.
In my case it returns “i386-pc-nto-qnx6.3.0”.
So I could start configure like this:
./configure --build=i386-pc-nto-qnx6.3.0 --host=i386-pc-nto-qnx6.3.0
The config.guess script works fine on my machine even without automake or autoconf installed.
If you use QNX 6.3 you can download these tools as repostories from the QOpenCD website.
For QNX 6.21 they should be available in the third party repository (Something like ‘gnu autoconf’ I guess).