There are discussions of this on various websites, e.g., http://boards.straightdope.com/sdmb/showthread.php?t=236445 where a few transcriptions and translations are offered. It says Stills varied the lyrics when performing live, but the recorded version goes

¡Que linda! Me recuerda a Cuba
La reina de la Mar Caribe
Quiero sólo visitarla allí
Y que triste que no puedo. ¡Vaya!
O Va! O Va!

Another poster in that thread gives

Que linda me la traiga Cuba,
la reina de la Mar Caribe.
Cielo sol no tiene sangreahi,
y que triste que no puedo vaya,
Oh va, oh va, va.

Loosely translated that is:

How happy it makes me to think of Cuba,
the smiles of the Caribbean Sea,
Sunny sky has no blood, and how sad that
I'm not able to go
Oh go, oh go go

but also offers the translation,

What beauty Cuba brings me,
The queen of the caribbean Sea,
There's no blood in the sun or sky.
Oh, how sad I cannot go.
Oh go, oh go, go.

Then someone else suggests a better translation of the last part would be

The heavenly sun has lost its blush.
It is sad that I cannot go.

Typing

suite judy blue eyes spanish

into Google will get you any number of other discussions.