Not sure if 3 bedrooms is enough (or your budget) but highly recommend this airbnb -
Good location and hosts are great. We stay in Dublin often and it is hard to find something large enough for a group your size. When we are a smaller group we stay in the center of the city but Portobello is close enough if you need the space. Stayed there recently when we went as a family.
I strongly recommend the jail (gaol). You need to book 28 days before and book right at midnight Dublin time. If you miss, you can book last minute and tix are generally available.
I’m not a huge fan of the Guiness tour but it seems to be a must for most people visiting Dublin. Our kids wanted to go so we have now done it several times. We prefer the Jameson tour/experience.
If you want to see everything there is - I would recommend the Go City card. You can do an all inclusive (based on number of days) or a pick a number of things you want to see. If you are going to do several of the museums/activities on the card it makes sense vs rack rates. If you do - start with the Big Red Bus and take the whole loop - gives you a feel for what’s where and some of the tour guides are quite good.
If you’re into music (or the kids are) the rock and roll museum is pretty good.
Depending on the ages of the kids stop into the Temple Bar for a drink (even just a soft drink). It is a really touristy area but experiencing an Irish pub is a must. There is often live music and it is always hopping.
I found the Jeannie Johnson tour really interesting - if you like history.
I can give you views on the museums and other attractions if you want and provide other recs depending on the ages of the kids and what you guys enjoy. Was there last month with my 2 twenty something kids and - despite really awful weather - we had a great time. Feel free to reach out if you’re looking for specific recs.