I think the German Embassy rsp. the responsible consulate for Puerto Rico should be able to help you. They may not get the birth certificate but they can give you the right contacts in Germany. According to the web site of the German ministery for foreign relations the contact info ist:
Telefon (001 305) 358 02 90
Fax (001 305) 358 03 07
Postal address: Consulate General of the Federal Republic of Germany, 100 N. Biscayne Blvd., Miami, FL 33132-2381, USA.
E-Mail miami@germany.info
Website http://www.miami.diplo.de
In General the "Einwohnermeldeamt" ("registration office for residents") of the birthplace will give you a birth certificate. If you simply address a letter to:
Einwohnermeldeamt
Munich
Germany
it will arrive, although the postman may need some time more.
Simply write them;
Sehr geehrte Damen und Herren,
bitte senden Sie mir 3 Geburtsurkunden zu.
Dear madam, dear sir, please send me 3 birth certificates.
Then write name, date of birth ("Geburtstag") and location of birth ("Geburtsort"), if possible also the last address of residence ("letzte Wohnanschrift"), name and birthdate of parents for proper identification.
But you can be quite sure that they can read an English letter, too.
I suggest you phone the consulate first.
As someone else suggestet you may contact your Embassy in Germany. Actually it should be their job to help US citizens. In Berlin the phone number is +49 30-8 30 50
Fax + 49 30-2 38 62 90.
Probably the better address is the consulate general in Munich which is responsible for Bavaria (inkludes Dachau):
Tel. +49 89-2 88 80
Fax + 49 89-28 30 47
Postal address Königinstraße 5, 80539 Munich, Germany