They're totally different. What do you want your board for?
Penny boards are ment to get around easily in urban areas, roll roads and sidewalks. They're light, cheap and convenient. But you can't do much more than roll around in them, and they're dangerous at high speeds, and they break fairly easily if you use them for anything other than rolling around.
Long boards are pretty awful for everyday use and city circulation, they're made for high speed on large, empty straight roads and when you get better at it, turns. They're a lot more comfortable though,and more sturdy, but also more expensive, + grip care and whatnot and harder to master.
Tl;dr it depends what you want the board for.