Hi. I'm from SD and would second the suggestion to stay at either the Bahia or Catamaran - depending on your budget really. They are both on the bay, across/down the street from the beach.
**Paradise Point is wonderful too of course, it's a proper upscale resort and very, very nice as well as on the bay. But you will need to drive to the beach (parking though will 100% not be an issue in October - there are huge parking lots in Mission Beach.) And of course the Hotel Del is simply awesome. If your budget allows for this, then do that and you won't regret it. But it's pricey.
The Cat is an upscale resort with some ocean view rooms and is very nice. It also has more dining options - both onsite and nearby. Anyone should be happy there.
The Bahia has lovely grounds and the rooms are clean, but "standard" if you know what I mean. Nothing plush or fancy. But the west-facing bay front rooms are great - you're basically walking right out to the sand and the bay. I would not stay in the east facing rooms though as I have heard they are in need of a remodel.
What's also neat is that there is a ferry boat (people only, not cars) that circles the bay hourly with docks to board/disembark at these 2 hotels. Rides are complimentary if you're staying at either resort.
Also, with a 2 year old, you may enjoy the bay at either hotel even more than the ocean because there are no waves. There's just a lot more freedom for the toddler set to run around and enjoy the bay's beach due to this. And the water conditions at the bay are the best in recorded history this year thanks to the unfortunate drought (no rain = no runoff = pollution not flowing into the bay.)
Have a great trip wherever you end up staying!