If I have the power company disconnect their lines from my house, can I remove the meter, and connect the Generator directly to my house through the outside box where the meter was? It has 3 basic wires, I'm assuming a 1 is the ground and the other 2 are + and - wires.

One is the neutral that also serves as the equipment ground, the other two at hots.
Yes, provided your generator can produce the same power as what you need, you can connect a generator your home. It's done all the time even with the power company still connected.

A better way is a transfer switch.

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A better way is a transfer switch.

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If the utility is completely disconnected what is he transferring?

Of course, if there is ever the possibility of reconnecting to the utility then yes, you are correct.

Well the OP did not say why and a generator in not likely to be powerful enough for a whole home. And even if it was it's still not cost effective compared to the grid. So really the best way is a transfer switch on a critical load panel. That way you only have the loads that the generator can handle.

BTW there should be four wires from the 230v outlet on the generator labeled W, X, Y and G for neutral, hot 1, hot 2 and ground. There are not positive and negative with AC. The hot are opposite sine wave 230v from each other and 115v from neutral/ground.