The ending cutscene shows Zelda in Hyrule castle, Link is seen alone in that boat.
True. That is in fact the order of the scenes shown at the end of the game. However, the manual itself implies that LA does not come after or have any relation to the Oracles.
Taken directly from the Link's Awakening manual:
Prologue (on pg.3)
Though you fufilled the Hyrulian prophecy of the Legendary Hero and
destroyed the evil tyrant Ganon, the land of Hyrule enjoyed only a
precarious peace. "Who knows what threats may arise from Ganon's
ashes?" the restless people murmured as they knitted their brows and
shook their heads. Ever vigilant, you decided to journey away from Hyrule
on a quest for enlightenment, in search of wisdom that would make you
better able to withstand the next threat to your homeland. Months of
difficult travel passed. After a long and fruitful voyage, you breathed
deeply the sea spray from the deck of the ship that carried you home to
Hyrule. But your homecoming was not to be. Suddenly a squall struck
your ship, and though you valiantly fought the waves, a lightning bolt
reduced your ship to splinters. Your world faded to black as you sink
into the darkness of the storm-tossed.
This clearly states a continuation of the same Link who defeated Ganon, venturing off to clear his mind. Seeing as how the game comes right after ALttP, it easy to see that LA is the sequel.
Now here is the story from the manual of Oracle of Seasons:
A NEW CHAPTER
One day in Hyrule, a strange force drew Link deep within Hyrule castle, where he found the Triforce resting, glittering brilliantly as it awaited him.
"Link... Link... Accept the quest of the Triforce!"
Suddenly, Link was enveloped in a shaft of light, and the next moment, he vanished.
When Link awoke, he found himself in a forest he had never seen...
The manual goes on to tell more about how Link had ended up in Holodrum.
But the point of this is that the LA manual clearly shows a continuation from its previously released title, while the Oracle of Seasons manual tells of a new story. Link is drawn into Hyrule Castle by a "strange force", which implies that he did not recognize the force. It wasn't until he actually saw the Triforce that he realized what force was pulling him to his destiny in the Oracle games, while in LA, Link had already known about the Triforce.
If Link's Awakening were to take place after the Oracle games, then the entire manual prologue of LA wouldn't make any sense. Yes, Link does in fact defeat Ganon at the end of the two Oracle titles, however this all took place in Labrynna/Holodrum, and not Hyrule. The LA manual clearly states that the people of Hyrule were the ones scared of Ganon's return, thus it talks about the events of Link defeating Ganon in ALttP.