Your updated question mentions axle holes are not an option for your needs, and just pin holes are allowed. There's no LEGO part (I know of) with that exact topology, nor do I see a way of combining parts to achieve the desired topology within a 3L size restriction.
If none of the below suggestions suit your exact needs, and assuming cutting off the pins of a 48989 part is not an option, then non-LEGO parts are your only option it seems. I'll have to defer to someone else in that case. I'll leave this answer up, since it might provide inspiration.
LEGO Technic connectors with 90 degree offset holes, limited to 3L size (but with axle holes)
The closest is probably Technic, Axle and Pin Connector Perpendicular 3L with Center Pin Hole, albeit with axle holes rather than pin holes :
There exist similar parts as well, like eg. Technic, Axle and Pin Connector Perpendicular 3L with 2 Pin Holes :
Or the smaller Technic, Axle and Pin Connector Perpendicular :
LEGO Technic connectors with 90 degree offset holes, with just pin holes (but exceeding 3L size)
There are some parts that have just pin holes, offset by 90 degrees, like Technic, Pin Connector Perpendicular 2 x 2 Bent :
Or the bigger and more recent Technic, Pin Connector Block, Liftarm 1 x 3 x 3 :
Or even Technic, Liftarm, Modified H-Shape Thick 3 x 5 Perpendicular :