Looks like you need to generate the power spectrum of the input signal and compare that to the spectrum of the output. Look in Signal Processing Toolbox (help "spectrum") for various ways of computing signal spectra.
BODE plot is really for looking at the frequency response of a system (the low pass filter in your case). Since you do not know this system, you will need to "estimate" it using the input/output signals that you have recorded. This you can do by using identification routines in System Identification Toolbox (see tfest in R2012a for example, or procest/pem/n4sid in older releases). Then you can use the "bode" command to view the mag/phase of the frequency response of the estimated model.
For model-free (non-parametric) generation of frequency response from I/O signals you can also check out tfestimate (Signal Processing Toolbox), spa/spafdr/etfe (System Identification Toolbox).
