I would think train would be the fastest, and since driving in the city is just horrible you probably won't want to have your own car.

Two small children = drive yourself in your own car according to the most direct route.
The subway/bus/train connections are not as convenient as they could be, especially with small children—don't waste the time.

Drive north from Baltimore and cross into NYC at the George Washington Bridge. (Newark Airport will be along the way if you are collecting your brother.) The GW Bridge feeds onto the Cross Bronx Expressway, which intersects the Bronx River Parkway after a few miles. You'll be heading for the Bronx River Parkway entrance to the zoo, the most convenient when coming by car.

From the zoo's website:
For Drivers Using GPS
Using a GPS unit to navigate to the zoo? We have two main parking lots, one at Southern Boulevard and the other off the Bronx River Parkway. ... To get to the Bronx River entrance, please use the intersection of Bronx River Parkway and Boston Road, Bronx, NY 10460 as your GPS destination.

From New Jersey
Most direct route:
George Washington Bridge to Cross Bronx Expwy (I-95) to Exit 4B. Follow signs to the Bronx River Pkwy North (you’ll be bearing left after the I-95 entrance ramp). The Zoo’s Bronx River entrance (Gate B) is located at exit 6 off the Bronx River Pkwy.

Train will not be fastest. The train from Baltimore goes to NY Penn Station. You would have to make a convoluted series of subway connections and a 45-60-minute ride from there to the zoo. Much easier to drive all the way.

Following the directions provided, you will be on fast highways until you reach the exit for the zoo. Certainly there will be some traffic issues, especially at the bridge, but to my mind a driving all the way would still be better for your family.

I would drive and meet your brother by the entrance by the parking lot by the Bronx River Parkway.

Sounds great - if I park at the zoo, which closes ~5, when we'll be going - is there more to explore nearby? I'm hoping to have something more than kid-fare for lunch or the ride home.

We're at the National Zoo in DC a few times a year, so we usually stop in Chinatown there, and wouldn't mind finding someplace fun nearby for a quick bite or well-packed to-go (oldest nephew plays football + preteens so takeout won't be an airport issue

The zoo is an oasis in a still gritty neighborhood of NY. You will enter on the parkway side. Possibilities for lunch elsewhere would be all the way to the other side of the zoo—not worth the effort in my opinion. For lunch during your visit, it would be better to stay in the zoo and buy lunch or pack your own lunch.

Dinner possibility . . . your best bet for other food options nearby might be Arthur Avenue, the "Little Italy" of the Bronx. It is nearby, but would require driving from zoo parking, finding your way on local streets and then finding parking. I'm not sure I'd recommend it for a family.

There's a McDonald's at Fordham Road and Southern Blvd at the northwest corner of the zoo, but for dinner you'd probably have to go by car anyway since the zoo parking lot will close.

Thanks for the candor and the responses. The last time I was in the Bronx was Post-9/11 for Cal Ripken's last game - it was a long one - at old Yankee Stadium. This was grittiness then, so this is good to know.

Central parking is advertising $4-5 for nearby parking - which was enough for me to think that the Renaissance hasn't hit the whole area yet.

Once again I agree with Ellenem. Arthur Avenue is wonderful but it is difficult to park and navigating the streets of The Bronx for the unitiated may be difficult.

I have not been to the zoo since last year, but I do not remember any food beyond the usual kids stuff and what the gorillas eat.

The best options for "adult" food at the zoo will be found at the Dancing Crane Cafe, which is actually a pretty nice setting. I can't speak about the quality of the food. Other food available at food stands will be the typical fare attractive to kids.

http://www.bronxzoo.com/plan-your-trip/dining.aspx

Public transit from the Bronx Zoo to EWR would be a horror - way too many changes for them to get back to the airport. But your driving them to EWR will also be difficult - since rush hour is 4 to 7 pm and you will be going through part of it - across the GWB.

I think driving is the lesser of two evils.

O'Dark thirty out of Baltimore will put you into GWB traffic near the tail end of quarter past rush hour. Really no way around that.

When we visit the Bronx Zoo we always pack a picnic lunch & waters in a small backpack. Schlepping a cooler (hard or soft) is too much work unless you have a stroller. I don't recall if BZ has restrictions on what food you can bring into the park or not.

The weather for later this week is supposed to be beastly (record) hot - over 95 on Thu., but projected to cool off for Friday. Who knows. If it's beastly hot on Friday you may want to bug out of the zoo mid afternoon. That means getting to the zoo by around 10:30 or 11 at the latest would be good.

Driving back to NJ you'll hit the evening rush hour - that's likely to be worse so make sure your brother's family budgets plenty of time. It may take an hour to get from Bronx Zoo across the GWB. Compounding the problem is the Yankees have a home game this Fri @ 7pm, which means additional traffic for the several mile stretch from Bronx river pkw past the stadium towards the GWB.

There might be a better way to exit NYC but I'd need to think about it. Maybe head NORTH on the BRP to the cross county pkwy, then south on I-87 to the bridge. Probably 6 of 1, 1/2 dozen of another.

Sorry - my directions are incorrect.

Bronx Zoo is just north of I-95, the Cross Bronx Expressway which goes straight line across the GWB. You would not pass by Yankee stadium, and going north to the Cross county would NOT be a good idea.

I was thinking of the Bruckner / I278. You may get stuck in traffic but at least it would be a straight shot across the bridge and probably not too bad.

Except for trying to make your way thru a city that your not familiar with in your car with all the worst drivers trying to kill you. The train would be the easiest just hop on and go. Even if you had to change trains your only going for 1 day so 1 kid per hand.