Best train from Lucerne to Wengen after flood damage?

Yes. See www.sbb.ch for options.

You will see two options on SBB between Luzern and Interlaken Ost: one is the regular scenic train over the Brunig Pass to Meiringen and substitute bus from there; the other is train to Olten, changing there to a train going to Interlaken Ost.

The latter “two train” route is less scenic than the Brunig Pass route. But if you choose the scenic train route, you will end up in a tunnel for most of the bus portion. At least that is what I have read.

Yes, the bus goes through the tunnel, so the beautiful portion along the lake of Brienz is out for now, but the rest of the scenic train journey is still pretty impressive. Going over Olten is longer and more expensive.

I've just been down to Interlaken and saw the substitute bus service there. It appears to be well organised, and they have enough busses so that everyone has a seat. Do pay attention with bus you take though. There are direct busses that do not make any stops en route, and there are busses that also stop in Brienz. The latter take longer, and thus cannot guarantee you make any connections at either end.

How long is the bus service replacing the train service expected to last?

mmittleman,
THAT is the CHF million question!
I have a AirBnB in Brienz booked for exactly 4 weeks from now!
Tomorrow is just 2 weeks from the flood event.
No one is making any projections just yet ;-(

Latest news is that the interruption will last till at least 29 September. The repairs needed to the track are not trivial, and the railway plans to completely rebuild 1,5 km of line.
So it is possible that it even is going to take longer.