It depends on what you want to do with the computer. The 3870 will be like 50% faster in DX 9 games like the CoD series and such, however it is below most modern games minimum system requirements.
If your not into games the GPU built into haswell has some advantages such as video encryption and transcoding that will be better than the old 3870.
So for normal computer usage just go onboard.
For older dx9 games go 3870.
If you want to play newer games drop $100 on a HD7770 or a GTX650.
The ATI 3870 is better than the old Intel HD4000 graphics, and as the HD 4600 is meant to be somewhat better, it will certainly be closer in terms of performance. Running a separate GPU will take the task away from the processor. The chart below may help.