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In terms of ERA, it seems as if it really doesn't matter who the Yankees catcher is, since 2004:

Year	Last	 First	Inn	ERA	
2007	Phelps	 Josh	1	0.00	
2004	Navarro	 Dioner	13	1.38	
2008	Posada	 Jorge	27	2.00	
2005	Nieves	 Wil	9	4.00	
2005	Flaherty John	345	4.12	
2006	Posada	 Jorge	1050	4.37	
2007	Nieves	 Wil	169	4.37	
2006	Stinnett Kelly	222	4.39	
2007	Posada	 Jorge	1111	4.50	
2007	Molina	 Jose	169	4.62	
2004	Posada	 Jorge	1102	4.65	
2005	Posada	 Jorge	1077	4.67	
2006	Nieves	 Wil	19	4.74	
2006	Fasano	 Sal	153	4.83	
2004	Flaherty John	328	4.93	
2008	Molina	 Jose	36	5.00	

A third of a run difference, here and there, doesn't seem huge.

But, there's something else to consider here. Check out the numbers for WP+PB per game:

Year	Last	First	Inn  WP+PB/G
2006	Nieves	 Wil	19     1.421
2007	Posada	 Jorge	1111	.526
2008    Molina	 Jose	36	.500
2004	Posada	 Jorge	1102	.482
2006	Posada	 Jorge	1050	.428
2005	Posada	 Jorge	1077	.343
2007	Molina	 Jose	169	.319
2004	Flaherty John	328	.302
2006	Stinnett Kelly	222	.244
2006	Fasano	 Sal	153	.236
2007	Nieves	 Wil	169	.213
2005	Flaherty John	345	.183
2008	Posada	 Jorge	27	.000
2004	Navarro	 Dioner	13	.000
2005	Nieves	 Wil	9	.000
2007	Phelps	 Josh	1	.000

Over the last four seasons, Posada is good for at least one wild pitch or passed ball (just about) every 2.25 games played behind the plate. And, that could be the rub as to why some Yankees pitchers prefer to pitch to someone other than Jorge - if it's true that some don't like throwing to him. It could be possible that some pitchers see those PB and/or WP as plays that should be made - and situations that they just don't want to deal with when they happen...maybe.