The harbor building option should be a resource that appears near the coast, like gold mines and other stuff appear after being researched. So ya, Option 1.

I get alot of harbours up (:
In my last game I think 8 of my 10 cities had beaches (:

But then again it was one one of my custom  maps

That's easy enough to do with a quick mod, just toss this into an xml file in the Mods folder.

<ImprovementTypes>
    <ImprovementType InternalName="K_Harbor">
        <SupportedTerrainType>Land</SupportedTerrainType>
        <SupportedTerrainType>City</SupportedTerrainType>
    </ImprovementType>
    <ImprovementType InternalName="E_Harbor">
        <SupportedTerrainType>Land</SupportedTerrainType>
        <SupportedTerrainType>City</SupportedTerrainType>
    </ImprovementType>
</ImprovementTypes>

You can build harbors anywhere, in any city, but the ship won't be able to move out to sea unless you use raise land on a cliff, then build on that tile to connect your city to the ocean (best to just build the harbor on that tile). It's not exactly very intuitive, IMO.

But can't we just Raise Land more often to build an entire bridge to the new continent, making harbors absurd and obsolete?

Well, to rub salt in the 'AI has no concept of naval invasion' wound, there are no military naval units military units or naval battles.  That was enough for me for them to be 'obsolete'.