As mentioned in the comments this answer produces results too slowly and the pebbles are not that smooth, but since I did go through with the idea (which I find interesting) I am posting the outcomes.
The idea for making a random pebble is to generate random points that would determine pebble's shape and then use a 3D quantile envelope to derive pebble's surface.
Here we generate the random points in such a way that they determine the pebble shape:
data1 =
RandomVariate[
MultinormalDistribution[{1, 2,
3}, {{3, 0, 0}, {0, 1, 0}, {0, 0, 2}}], 1*10^4];
data2 =
RandomVariate[
MultinormalDistribution[{1, 2, 2/5},
0.8 {{1, 0, -1/2}, {0, 1, 0}, {-1/2, 0, 2}}], 1*10^4];
data = Join[data1, data2];
Dimensions[data]
(* {20000, 3} *)
Making random variate mixtures with different distributions and parameters (means/centers, variations/correlation matrices) would bring different pebble shapes.
Some additional rotation (optional):
rmat = RotationMatrix[Pi/3., {{1, 1, 1}, {1, -1, 1}}];
data = data.rmat;
Plot the generated random points:
Block[{qs = 12},
qs = Map[Quantile[#, Range[0, 1, 1/(qs - 1)]] &, Transpose[data]];
ListPointPlot3D[data,
PlotStyle -> {PointSize[0.002]}, PlotRange -> All,
PlotTheme -> "Detailed",
FaceGrids
-> {{{0, 0, -1}, Most[qs]}, {{0, 1, 0}, qs[[{1, 3}]]}, {{-1, 0, 0},
Rest[qs]}}]]

Find the directional quantile envelope:
Import["https://raw.githubusercontent.com/antononcube/MathematicaForPrediction/master/QuantileRegression.m"]
AbsoluteTiming[
qreg = QuantileEnvelopeRegion[data, 0.95, 78];
]
(* {4.57647, Null} *)
Discretize the obtained region in order to plot it:
AbsoluteTiming[
bdreg = BoundaryDiscretizeRegion[qreg];
]
(* {168.562, Null} *)
The command above will take less time if smaller number of directions in QuantileEnvelopeRegion
are used. (The third argument.) The obtained pebble might have some very flat, angular sides.
Plot together with a sample of the points:
Block[{testData = RandomSample[data, 4000]},
Show[{ListPointPlot3D[testData,
PlotStyle -> {Gray, PointSize[0.006]}], bdreg}]]

Just the pebble by itself:
bdreg

Probably some further refinements or manipulations of the obtained discretized region can be made in order to derive smoother surfaces.