A three-dimensional scatter plot is good, but can sometimes be hard to interpret because you lose a dimension of information when you project it onto the two-dimensional page.
An alternative is to do multiple two-dimensional scatter plots. This is equivalent to making a three-dimensional plot and then looking at it from different angles. For example, in R you can generate some data using
> X = rnorm(100)
> Y = rnorm(100) + X
> Z = rnorm(100) - X
and collect it together into a single data frame object
> D = data.frame(X=X,Y=Y,Z=Z)
You can generate the sample correlation matrix with
> cor(D)
X Y Z
X 1.0000000 0.7647313 -0.7487290
Y 0.7647313 1.0000000 -0.5407474
Z -0.7487290 -0.5407474 1.0000000
and finally generate the set of two-dimensional scatter plots
> plot(D)
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