Hello Vikram

As you know both these colleges are most prefered for Engineering and hence they are not much preferred for MBA. 

If choosing between these comes into the table then please go for BIT Mesra as it is somewhat better than MNIT Jaipur according to me.

In 199 CMAT there are other B-school which is wholly based on MBA

1 XISS Ranchi

2 MIT Pune

3 UPES Dehradun

4 School of Communication, Cochin

5 Jaipuria Institute of Management.