3.0i is a 230hp M54 engine which is robust and in many, many E46 generations of cars.
The 3.0si is a 265hp N52 which isn't as heavy duty but is still very reliable.
However the 2 engines do have different characters where the M54 is slightly more lazy but the N52 does like to rev.
They sound different too, the M54 is more bassy and boomy and the N52 has more of a "zing" to it (think almost E46 M3 esque)
Performance wise there isn't a great deal in real world performance but you're looking at about 1 second difference in the 0-60mph and the N52 being slightly more flexible in terms of in gear performance.
I would drive both and see which you prefer as you will pick up a really nice 3.0i for 5k but probably a shabby 3.0si for the same cash.
Good luck with the search