Yes, you are still discarding, the card just goes to a different zone. The Oracle text of the Library should also make that quite clear:
If an effect causes you to discard a card, discard it, but you may put it on top of your library instead of into your graveyard.
Edit:
Sorry, I was wrong there. While you are still discarding the card, it does not get revealed, so the Miser's abilities cannot see, what you've discarded and won't trigger.
From the Library's rulings:
10/4/2004 Since the card goes directly to the library, the card is not revealed unless the spell or ability requiring the discard specifically says it is.
"If a card is discarded, but an effect causes it to be put into a hidden zone", such as the library (C.R. 400.2), "instead of into its owner’s graveyard without being revealed, all values of that card's characteristics are considered to be undefined" (C.R. 701.8c, 400.2), including at least whether that card is a "creature card" or a "land card" for purposes of Bone Miser's first or second abilities. This is not the same as the card having no characteristics (compare C.R. 701.8c with C.R. 406.3a). See also this thread.
EDIT (Feb. 4, 2021): Edited to conform to rule update for Kaldheim.
EDIT (Jan. 11, 2023; Dec. 25, 2023): Correctness edit.
Yes, you are still discarding, the card just goes to a different zone. The Oracle text of the Library should also make that quite clear:
Edit:
Sorry, I was wrong there. While you are still discarding the card, it does not get revealed, so the Miser's abilities cannot see, what you've discarded and won't trigger.
From the Library's rulings:
Former Rules Advisor
"Everything's better with pirates." - Lodge
(The Gamers: Dorkness Rising)
"Any sufficiently analyzed magic is indistinguishable from science."
(Girl Genius - Fairy Tale Theater Break - Cinderella, end of volume 8)
EDIT (Feb. 4, 2021): Edited to conform to rule update for Kaldheim.
EDIT (Jan. 11, 2023; Dec. 25, 2023): Correctness edit.