If your source uses paragraph numbers instead of page numbers or line numbers, your in-text citation should give the relevant number or numbers preceded by par. (for paragraph) or pars. (for paragraphs):

HAMLET. Ay, marry, is ’t,

But, to my mind, though I am native here

And to the manner born, it is a custom

More honored in the breach than the observance. (par. 25)

To allow readers to easily locate the quotation in a more standard edition of the play, you could add the act, scene, and line numbers in square brackets as part of your citation:

HAMLET. Ay, marry, is ’t,

But, to my mind, though I am native here

And to the manner born, it is a custom

More honored in the breach than the observance. (par. 25 [act 1, scene 4, lines 15–18])

For either method, it would be a good idea to indicate in an endnote that your source does not have line numbers, because readers may expect them.