Hi Kailoe
There is a glass bottom boat trip in Alcudia you can book this through one of the Bureau De Changes or your rep.
They are fine as you can take the little ones underneath so they can see the sea and fishes when its stationary.
They usually have sime for a swim but you dont have to do this.
If I was you though they are very young so will get bored after a bit so wouldnt do a full day boat trip, afterall looking at the sea through the glass gets a bit monotonous when your a toddler!
We did one in Greece once (fULL DAY) and it was so boring for them.(6hrs) long is far too much.
Have fun, there was a photographer on the one we went on in Alcudia and he took pics of you walking on to the boat.
Regards Liz.

There is a 45 min boat trip to Playa Formentor which I am sure runs from Alcudia. It certainly runs from Puerto Pollensa which is a 15 min bus trip away. At Formentor there is a nice beach with great swimming. Best combination is go out by boat and return by bus, you get the best of the sea and mountain views that way.