We recommend staying somewhere in the area around the pin, as it's within walking distance from the port (where tours depart), restaurants, Taraw Cliff, etc.
We stayed at these spots, 100% recommend them:
Cuna Hotel, the best hotel in our opinion. It has a rooftop pool and is smack in the middle of town!
Happiness Hostel, more budget-friendly, has a great vibe and is super social.
Here are other excellent options too:
Best luxury: The Funny Lion (El Nido). It's a hotel chain, excellent value for money. We stayed at their site in Coron and loved it.
Best for families and groups: El Nido Coco Resort. This resort is a 5-min trike ride from town. Has apartments, bungalows, and villas, fully equipped. Villas sleep 4-8 people.
Quick tip: Avoid scams by reading reviews first and do not book places without many reviews yet. We have never been scammed in the Philippines thanks to this.