I ran into this problem myself. I found that not specifying an input height, but using the font-height and padding combined, results in vertically aligned text.
For instance, lets say you want to have a 42px tall input box, with a font-size of 20px. You could simply find the difference between the input height and the font-size, divide it by two, and set your padding to that amount. In this case, you would have 22px total worth of padding, which is 11px on each side.
<input type="text" style="padding: 11px 0px 11px 0px; font-size: 20px;" />
That would give you a 42px tall input box with perfect vertical alignment.