That's a tough choice! Both look absolutely beautiful. A couple thoughts based on the other responses:

It does sound like El Nido might be a bit easier to navigate with little ones since Boracay requires that ferry ride each way, which could be tiring for a 2-year-old. Being able to just relax on the beach without too much traveling around would probably be ideal.

Did you have any particular resorts in mind for either location? Having an all-inclusive option that takes care of meals could make things less stressful too. Off the top of my head, I think El Nido maybe has fewer large resorts than Boracay, so availability could be a factor too.

Since relaxing and swimming are the main priorities, have you considered looking at resorts on other islands that may have a bit calmer, smaller vibe than Boracay? Somewhere like Coron or Apo might still give you the gorgeous scenery without quite as many crowds.