How many miles are on the vehicle? A rebuild would give you a completely refreshed engine and the $6000 doesn't sound much different from what I've seen for used engine prices that would have an unknown background. I'd lean towards the rebuild if you can go without the ride for the time it takes to get done.

2002 X5 3.0 314,600 miles
2014 428i 24,300 miles

2004 325i sold at 123,600 miles
2001 325i sold at 66,000 miles

1970 Firebird - Under restoration