There is no course textbook but some useful and relevant texts are listed below.
Durran, Dale R. Numerical Methods for Wave Equations in Geophysical Fluid Dynamics (Texts in Applied Mathematics Series, Vol. 32). New York, NY: Springer, 1998. ISBN: 9780387983769.
Haidvogel, Dale B. and Aike Beckmann. Numerical Ocean Circulation Modeling. River Edge, NJ: World Scientific Publishing Co., 1999. ISBN: 9781860941146.
Haltiner, George J., and Roger T. Williams. Numerical Prediction and Dynamic Meteorology, 2nd Ed. Hoboken, NJ: John Wiley & Sons, 1980. ISBN: 9780471059714.
Jacobson, Mark Z. Fundamentals of Atmospheric Modeling. Cambridge, MA: Cambridge University Press, 1998. ISBN: 9780521637176.
Kantha, Lakshmi H. Numerical Models of Oceans and Oceanic Processes. Academic Press; 1 edition, 2000. ISBN: 9780124340688.
Pedlosky, Joseph. Ocean Circulation Theory. New York, NY: Springer; 1st ed. Corr. 2nd printing edition, 2004. ISBN: 9783540604891.
A handy quick-reference for some methods is Numerical Recipes on-line.