How to plot lat-lon-rainfall in MATLAB?
What kind of plot do you want? 


  Lat = [25.5 26.5 33.5 34.5 35.5 36.5 41.5 42.5]; 
  
  Lon = [89.5 91.5 78.5 79.5 83.5 84.5 75.5 76.5]; 
  
  Rain = [110 120 122 135 114 116 145 120 110 110];
  
  figure();
  
  plot3(Lat,Lon,Rain,'o')


will give you a scatter plot with Lat being the x, Lon being the y, and rain being the z.

Also note that because your vectors are different legnths, you cannot plot them. You must have vectors of the same lenght to plot (each point must correspond to another point on the axis).

Other types of plots will require you to interpolate between the data points.  

If you want to plot it like in the comment below: pcolor is your best choice.

Say your Lat/Lon vectors have n points. Then to make an nxn grid, you can use the command


  [X,Y] = meshgrid(Lat,Lon);


This will give you the grid you want, as long as your Lat/Lon Vectors are spaced how you want. To get the 'color" of the pcolor, you will need to have a nxn matrix of rain values: you will need to know what those are at each point. If you do not know those, then then you cannot plot it in map view unless you do some form of modeling or interpolation. 

If you have an irregular shape, I would not use matlab. I would use Visit or Paraview, and there are many guides online on how to use this.

If you must use matlab, I would create "fake points" to make the grid a regular shape, and give them false rain values (such as NaN). I would then edit the plot in a postprocessor (photoshop) so that Only the irregular shape appears. 

The spacing of the grid does not matter as its specified via your vectors.