I want to use some unix tools on my rooted android arm6 based phone. I will be using cross compiler tools provided here. If I want to compile
Unless you particularly need to build against a more standard libc than bionic, you can just use the ndk's toolchain, either by copying the hello-jni example and changing BUILD_SHARED_LIBRARY to BUILD_EXECUTABLE in the jni/Android.mk or using the script to generate a stand alone toolchain. You may want to use the V=1 option to the ndk-build script to see the commands it's issuing to its gcc.
Otherwise you may need to pass the prefix to the configure script or manually edit it into the Makefile for the project. This often has not gone well as many projects have make systems not really set up for cross compiling, I've had to resort to editing the configure script to set prefixes and skip tests where it tries to execute a test program.
An option that sometimes works when the build system is more complicated than the project requires is to do a configure for your host (let's hope that's linux). Then manually edit the generated Makefile to change anything needed to build for android instead. Might not be a bad idea to do a clean just in case (especially if you did a test host build). And then do the build which will pick up the arm compiler from your Makefile modifications.
Lastly, if you can be content with the original netcat by Hobbit rather than the gnu version, you hardly need to port it to android yourself as that's already been done. There's already an android version in the google tree at https://android.googlesource.com/platform/external/netcat which may be on your device already (as 'nc'), and is definitely included in alternate ROMs such as Cyanogenmod.