First, I agree with a comment made by someone earlier - the toothpaste is only for taste. It doesn't help the cleaning, so I would just skip using it (obviously more difficult now that your son is familiar with it!). Water should be fine.
Next, one thing that worked well for my son was counting. He loves to count. So I'd give him the toothbrush to do it himself while I counted to 10. Then I'd get my turn to brush his teeth while counting to 10 (more slowly for my turn!). As he got older, we changed it to 20. So now he's 3 years old, and we count from 1-10 for the top and 11-20 for the bottom. It seems to work well because it's like a game and he knows there's an endpoint. And I don't let him off the hook until "20" (you might have to say "open your mouth again" a lot!). Also, I wait about 2-3 seconds between numbers - that way I'm able to accomplish 1.5-2 minutes of brushing time!
I noticed you also have a 4 month old. I would start earlier with her - I think part of why my son never minded the tooth brushing so much is because we started when he first started getting teeth. It's just part of the routine. (And we didn't add toothpaste until this past year so he didn't know what he was missing!).
One other thing - you can try other toothbrush gimmicks - we have one that you push the bottom and it makes the toothbrush flash red lights for 1 minute (so it's another way to make it fun AND make sure you brush long enough)...I forget what it's called but they have them at CVS, I think. Another one like that is called "Tooth Tunes", by Oral B. It's ridiculously expensive ($10 for single, non-rechargable brush that has no replacement head). But it's fun - it plays a song for 2 minutes, but you can only hear it when you push onto the teeth to brush them. Ours plays "We Will Rock You"!
One other suggestion, going along with the toothbrush gimmicks (and this may get easier as he gets a bit older) is using the tool/trick of offering a choice. This works for MANY things with toddlers. Instead of saying to my son "Let's go brush your teeth," which offers him the opportunity to say "no", I say something like, "Do you want to brush your teeth today with the light-up toothbrush or the musical toothbrush?" ... This way his answer has to be to pick one. You can also do it in this way: "Do you want to get dressed first or brush your teeth first?"... They feel in-control because they've chosen what to do. I love this trick!
Sorry to be so long-winded! Hope this helps.