On the app, you can view the "real-time" schedule (boats every 30-60 minutes) and also purchase tickets, which saves you time if you're running to catch the boat or don't want to leave your kids alone at the back of the line while you run ahead to buy tickets from the machine! It's pretty cool the way it works - you purchase tickets on the app and then when you're about to board you activate them. You show the screen as you board the boat to show how many active tickets you have, but nothing is scanned, they'll simply expire in 1 hour, which I guess is how the whole "free transfer" works if you're jumping to another line for a different destination? You can use the "trip planner" part of the app to see where to transfer, and unfortunately it looks like transfer timing may not be so great - for example you can transfer at Sunset Park to get to Rockaway, or at DUMBO to get up to Williamsburg, but you may have to wait a while unfortunately!
There was concern over whether or not you could keep your kids in the stroller on the boat, since the website says the boats have designated stroller parking areas. But, after having taken a ride, I can say yes, you can keep your stroller with you - on the bottom inside (temperature controlled) deck anyway. There are some seating areas at the end that can fit a bunch of strollers with the kids still in them. In addition, the two aisles are very wide so it doesn't seem like parking a single stroller next to a seat on the aisle would be a problem either - you can see someone's done that in the picture below right.
We've taken quite a few ferries and I've never before experienced this amount of rocking. My son, who gets car sick, felt rather ill. By the time we finished our 40 minute journey I wasn't feeling great either, thinking back on it I probably should have avoided using my phone and instead kept my eyes on the horizon. Anyway, if you or your family experience motion sickness, consider taking a dramamine or wearing sea bands.
A few of the seating areas have little tables you could use for eating or playing games. I saw a few outlets around so if you were in dire need to charge a phone you could. There are bathrooms, and a changing table for the babies!! There were signs that wi-fi is coming soon. And there was a nice concession stand with all kinds of snacks, alcoholic (and non-) beverages, iced coffee, and even some random games like UNO. They really thought of everything!!
With Bay Ridge being the first station of the South Brooklyn line, there's probably not a big problem getting on the next ferry, except maybe during rush hour. But returning home is another story. We got on around 5:30pm at Brooklyn Bridge Park Pier 1 Station and noticed them counting how many people came off the boat, and then announced they could take on 28 passengers. Well, lets just say there were plenty of people who did not get on and weren't too thrilled with having to wait an hour for the next boat. Ouch. So... don't wait to run to the dock at the last second. Consider getting in line with PLENTY of time to spare, or sending ahead someone to take one for the team and wait in line for you.
Sure, it's not free like the Staten Island Ferry, but it offers amazing views and a fun travel experience unlike anything you'll find on the MTA buses and subways, and for the same price! From Bay Ridge, you get a really great view of the Statue of Liberty and South Brooklyn. If you can part with your stroller and the weather is nice, head up to the top deck and breath it all in!