Which is more correct?
Now I am the main stakeholder...
I am now the main stakeholder...
Do the intonations imply different meanings?
Neither is more correct. They mean different things.
You first example can be interpreted like so:
Which means you are about to make a pronouncement about how things will be with you are the main stakeholder.
As a statement by itself it can be used to mean I am now the main stakeholder, but you have to put emphasis on now and make it seem like you are marking the the moment. A similar idea would be to make a future announcement:
Of course, if you put a comma just after now you get a different meaning:
This is using now as an interjection, it doesn't really mean anything with regard to the sentence. The rest of the sentence is just a statement explaining who you are.
Your other example
is a statement explaining that from this moment you are the main stakeholder. This structure can be used in a triumphant way, as an exclamation, for example:
or in a dry factual way:
I agree with the points made by Matt, but wanted to add the following:
If you start the sentence with a designation of time, you emphasize the time.
This first sentence is best used if time is somehow contextually relevant. For example:
In contrast, your other example emphasizes either 'I' or '(the main) stakeholder', depending on context.
The difference is negligible, however.