OK. Couple of things.
- As you said, Númenor is closer to Atlantis.
- But Númenor is not supposed to be heaven, the Grey Havens are, their name in Elvish: Valinor. They are also reachable by boat, BUT ONLY BY THE ELVES (and special others such as the wizards and the ring-bearers). Man dies and has a fate which is not known to any save the highest of the Valar and Ilúvatar himself.
- Valinor was once a part of earth, but it was effectively removed during the second age.
Now, as to the rest of your question.
The image of water = death is actually cross cultural (the river Styx anyone?). The obvious, "baptized into his death" is the clearest, most obvious Christian analysis (cf. Rom. 6). But that is not the only point which is made about water.
As an immediate example in Narnia (there are actually several such, but it would take a good deal of work to make them more obvious): in The Voyage of the Dawn Treader, they know they are close to the country of Aslan when they get to the place where the water is sweet. This means that the water is fresh and drinkable, as opposed to the salt water which can be found off of the coast of Narnia. In Revelation, the demons and powers of evil are all associated with saltwater. A "river of life", however, is associated with Christ and goodness.
Perhaps another example might be that Lewis had the witch in Silver Chair holding back a great underground flood. This actually seems to be a second variant on the same point made above.
As far as the rivers of Lewis are concerned, most of them strike me as references to the rivers of the Tigris and Euphrates — the location of the Biblical Garden of Eden.
The problem comes in when you try to analyze Tolkien this way. Far better, I think, in the case of Tolkien to say that "across the sea" is more a reference to something very far away (that is how it is treated in the LotR). Yes, Valar is across the water, but it has not always been so. I suppose you could say that this is like how man walked with God in the garden, but once man was cast out he no longer had access, but I think that the metaphor grows very weak.
Most of the bodies of water dealt with in Middle Earth are rivers. There is some reference to the sea in the LotR, but it really isn't terribly important. You do find several rivers and streams, however: There is a stream in the forest of Tom Bombadil. There is a river guarding Rivendell. There is a lake which Gollum lives by. Long lake is a port of commerce (Lakeport) built in the shadow of Dale. The river is used to send products down to the Elves. None of these seem terribly important.
There is a river in the Shire (Brandywine in the shire, but Baraduin elsewhere). It represents the border between the familiar and the strange. One can find a little bit more importance in the steam that runs through Mirkwood. If you fall in, you will sleep and not wake up (for some time). The Anduin guards Minas Tirith and Gondor from attack from the East.
I actually have to say that I like @MasonWheeler's comment so much that I think I needed to add that with Tolkien, it really does seem more like it
is that a long ocean voyage is a good symbolic analogue for a one-way journey to a place you're not going to return from.