Having worked with the NDK in Android Developer Tools (Google's Eclipse Fork), it's pretty painful. It takes a long time to get the environment set up and working (somewhat) nicely. You have to get a plugin to debug via ADT, I used the ARM DS-5 debugger. It works, but it's not a good user experience.
I used to complain about certain niggles in Xcode, but having used ADT, I shall never complain again. Comparatively, using Xcode is a joy.
I used the Android NDK extensively for an app I wrote recently. The main reasons were for cross compatibility (future iOS port) and because a 3rd party library I needed was written in C.
If your new to the world of C/C++..then maybe its painful, but for me it was easy to get up and running. They use the GCC toolchain behind the scenes, with gdb as the debugger.
The NDK exists as a download for windows,OSX and Linux. I developed exclusively on OSX (10.8) (Using the android develop toolkit (aka ADT) which is basically a re-skinned Eclipse) and then enabled "ADB over IP" on my Nexus 4.
After a bit of setup (like adb connect 'local ip' ) the Android version of gdb (ndk-gdb) on the mac just "sees" your phone, finds the process and automatically connects.
If / when a crash would happen (and it happend a lot :) ) you get a stack trace, code line numbers, etc.
It might not be as simple as the GUI Xcode world, but it certainly works.
I've also got remote core dumps for my app, using Google's Breakpad. When the app crashes natively it uploads a core dump to my server, where I can examine what happened. Here as well you get full stack dumps, line #'s, etc.
As far as a cross-toolchain goes, the NDK is quite nice. For the most part, it Just Works for compiling code. The multitude of STLs and complicated (behind the scenes) Makefile system can be annoying. However, the Makefile system is very simple for common needs. Debugging can be a pain, yes. Google is very diligent about releasing updates to fix bugs.
I used to complain about certain niggles in Xcode, but having used ADT, I shall never complain again. Comparatively, using Xcode is a joy.